dbSNP rs62064494: GAS7:c.1219-36G>A (chr17-9918135-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_201433.2(GAS7):c.1219-36G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0377 in 1,495,646 control chromosomes in the GnomAD database, including 1,300 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.034 ( 127 hom., cov: 33)

Exomes 𝑓: 0.038 ( 1173 hom. )

Consequence

GAS7
NM_201433.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.96

Publications

2 publications found

Variant links:

Genes affected

GAS7 (HGNC:4169): (growth arrest specific 7) Growth arrest-specific 7 is expressed primarily in terminally differentiated brain cells and predominantly in mature cerebellar Purkinje neurons. GAS7 plays a putative role in neuronal development. Several transcript variants encoding proteins which vary in the N-terminus have been described. [provided by RefSeq, Jul 2008]

GAS7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 17-9918135-C-T is Benign according to our data. Variant chr17-9918135-C-T is described in ClinVar as Benign. ClinVar VariationId is 1286767.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201433.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GAS7	NM_201433.2	MANE Select	c.1219-36G>A	intron	N/A	NP_958839.1	O60861-3
GAS7	NM_201432.2		c.1039-36G>A	intron	N/A	NP_958836.1	O60861-4
GAS7	NM_001130831.2		c.1027-36G>A	intron	N/A	NP_001124303.1	O60861-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GAS7	ENST00000432992.7	TSL:1 MANE Select	c.1219-36G>A	intron	N/A	ENSP00000407552.2	O60861-3
GAS7	ENST00000323816.8	TSL:1	c.1039-36G>A	intron	N/A	ENSP00000322608.5	O60861-4
GAS7	ENST00000585266.5	TSL:1	c.1039-36G>A	intron	N/A	ENSP00000464240.2	O60861-4

Frequencies

GnomAD3 genomes

AF:

0.0341

AC:

5192

AN:

152204

Hom.:

127

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0112

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.0279

Gnomad ASJ

AF:

0.0386

Gnomad EAS

AF:

0.00423

Gnomad SAS

AF:

0.0286

Gnomad FIN

AF:

0.0995

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0415

Gnomad OTH

AF:

0.0407

GnomAD2 exomes

AF:

0.0380

AC:

9095

AN:

239542

AF XY:

0.0393

show subpopulations

Gnomad AFR exome

AF:

0.0105

Gnomad AMR exome

AF:

0.0193

Gnomad ASJ exome

AF:

0.0395

Gnomad EAS exome

AF:

0.00203

Gnomad FIN exome

AF:

0.0987

Gnomad NFE exome

AF:

0.0451

Gnomad OTH exome

AF:

0.0467

GnomAD4 exome

AF:

0.0381

AC:

51240

AN:

1343324

Hom.:

1173

Cov.:

AF XY:

0.0384

AC XY:

25857

AN XY:

673764

show subpopulations

African (AFR)

AF:

0.0120

AC:

371

AN:

30822

American (AMR)

AF:

0.0194

AC:

844

AN:

43498

Ashkenazi Jewish (ASJ)

AF:

0.0396

AC:

999

AN:

25210

East Asian (EAS)

AF:

0.000998

AC:

AN:

39084

South Asian (SAS)

AF:

0.0284

AC:

2359

AN:

83194

European-Finnish (FIN)

AF:

0.0936

AC:

4779

AN:

51054

Middle Eastern (MID)

AF:

0.0573

AC:

317

AN:

5528

European-Non Finnish (NFE)

AF:

0.0389

AC:

39225

AN:

1008490

Other (OTH)

AF:

0.0409

AC:

2307

AN:

56444

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

2365

4730

7094

9459

11824

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1310

2620

3930

5240

6550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0341

AC:

5191

AN:

152322

Hom.:

127

Cov.:

AF XY:

0.0365

AC XY:

2722

AN XY:

74490

show subpopulations

African (AFR)

AF:

0.0112

AC:

466

AN:

41586

American (AMR)

AF:

0.0278

AC:

426

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0386

AC:

134

AN:

3468

East Asian (EAS)

AF:

0.00405

AC:

AN:

5190

South Asian (SAS)

AF:

0.0284

AC:

137

AN:

4824

European-Finnish (FIN)

AF:

0.0995

AC:

1056

AN:

10618

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0415

AC:

2820

AN:

68016

Other (OTH)

AF:

0.0402

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

257

515

772

1030

1287

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

186

248

310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0391

Hom.:

Bravo

AF:

0.0284

Asia WGS

AF:

0.0210

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.022

(source)

DANN

Benign

0.55

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over