Genetic Variant NM_201433.2:c.*3874T>C (chr17-9913354-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_201433.2(GAS7):c.*3874T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 232,094 control chromosomes in the GnomAD database, including 45,027 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.63 ( 31211 hom., cov: 32)

Exomes 𝑓: 0.58 ( 13816 hom. )

Consequence

GAS7
NM_201433.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.213

Publications

22 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 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
GAS7	NM_201433.2	MANE Select	c.*3874T>C	3_prime_UTR	Exon 14 of 14	NP_958839.1
GAS7	NM_201432.2		c.*3874T>C	3_prime_UTR	Exon 14 of 14	NP_958836.1
GAS7	NM_001130831.2		c.*3874T>C	3_prime_UTR	Exon 14 of 14	NP_001124303.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GAS7	ENST00000432992.7	TSL:1 MANE Select	c.*3874T>C	3_prime_UTR	Exon 14 of 14	ENSP00000407552.2
GAS7	ENST00000323816.8	TSL:1	c.*3874T>C	3_prime_UTR	Exon 15 of 15	ENSP00000322608.5
GAS7	ENST00000437099.6	TSL:1	c.*3874T>C	3_prime_UTR	Exon 14 of 14	ENSP00000410108.2

Frequencies

GnomAD3 genomes

AF:

0.632

AC:

96078

AN:

151982

Hom.:

31179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.777

Gnomad AMI

AF:

0.430

Gnomad AMR

AF:

0.548

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.611

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.558

Gnomad MID

AF:

0.529

Gnomad NFE

AF:

0.602

Gnomad OTH

AF:

0.590

GnomAD4 exome

AF:

0.583

AC:

46669

AN:

79994

Hom.:

13816

Cov.:

AF XY:

0.581

AC XY:

21406

AN XY:

36854

show subpopulations

African (AFR)

AF:

0.773

AC:

2950

AN:

3816

American (AMR)

AF:

0.555

AC:

1363

AN:

2456

Ashkenazi Jewish (ASJ)

AF:

0.452

AC:

2279

AN:

5044

East Asian (EAS)

AF:

0.579

AC:

6515

AN:

11258

South Asian (SAS)

AF:

0.450

AC:

312

AN:

694

European-Finnish (FIN)

AF:

0.559

AC:

266

AN:

476

Middle Eastern (MID)

AF:

0.586

AC:

280

AN:

478

European-Non Finnish (NFE)

AF:

0.588

AC:

28873

AN:

49126

Other (OTH)

AF:

0.576

AC:

3831

AN:

6646

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

925

1850

2774

3699

4624

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

224

336

448

560

<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:

0.632

AC:

96157

AN:

152100

Hom.:

31211

Cov.:

AF XY:

0.625

AC XY:

46448

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.777

AC:

32244

AN:

41496

American (AMR)

AF:

0.548

AC:

8378

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.459

AC:

1592

AN:

3470

East Asian (EAS)

AF:

0.610

AC:

3149

AN:

5162

South Asian (SAS)

AF:

0.454

AC:

2184

AN:

4812

European-Finnish (FIN)

AF:

0.558

AC:

5909

AN:

10586

Middle Eastern (MID)

AF:

0.510

AC:

149

AN:

292

European-Non Finnish (NFE)

AF:

0.602

AC:

40920

AN:

67970

Other (OTH)

AF:

0.586

AC:

1240

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1786

3572

5359

7145

8931

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

778

1556

2334

3112

3890

<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:

0.598

Hom.:

46661

Bravo

AF:

0.639

Asia WGS

AF:

0.556

AC:

1937

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.59

(source)

DANN

Benign

0.64

PhyloP100

-0.21

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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