Genetic Variant ST7:c.1254+7321G>A (chr7-117198257-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001369598.1(ST7):c.1254+7321G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 448,512 control chromosomes in the GnomAD database, including 104,320 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 0.64 ( 32153 hom., cov: 32)

Exomes 𝑓: 0.69 ( 72167 hom. )

Consequence

ST7
NM_001369598.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

Publications

6 publications found

Variant links:

Genes affected

ST7 (HGNC:11351): (suppression of tumorigenicity 7) The gene for this product maps to a region on chromosome 7 identified as an autism-susceptibility locus. Mutation screening of the entire coding region in autistic individuals failed to identify phenotype-specific variants, suggesting that coding mutations for this gene are unlikely to be involved in the etiology of autism. The function of this gene product has not been determined. Transcript variants encoding different isoforms of this protein have been described. [provided by RefSeq, Jul 2008]

ST7 links:

ST7-OT3 (HGNC:16045): (ST7 overlapping transcript 3)

ST7-OT3 links:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001369598.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ST7	NM_001369598.1	MANE Select	c.1254+7321G>A	intron	N/A	NP_001356527.1	H7BXS2
ST7	NM_021908.3		c.1254+7321G>A	intron	N/A	NP_068708.1	X5DRA0
ST7	NM_001369601.1		c.1254+7321G>A	intron	N/A	NP_001356530.1	E7EPD9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ST7	ENST00000323984.8	TSL:5 MANE Select	c.1254+7321G>A	intron	N/A	ENSP00000325673.3	H7BXS2
ST7	ENST00000265437.9	TSL:1	c.1254+7321G>A	intron	N/A	ENSP00000265437.5	Q9NRC1-1
ST7	ENST00000393451.7	TSL:1	c.1185+7321G>A	intron	N/A	ENSP00000377097.3	Q9NRC1-2

Frequencies

GnomAD3 genomes

AF:

0.644

AC:

97871

AN:

151992

Hom.:

32130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.547

Gnomad AMI

AF:

0.689

Gnomad AMR

AF:

0.759

Gnomad ASJ

AF:

0.790

Gnomad EAS

AF:

0.924

Gnomad SAS

AF:

0.765

Gnomad FIN

AF:

0.557

Gnomad MID

AF:

0.772

Gnomad NFE

AF:

0.651

Gnomad OTH

AF:

0.689

GnomAD4 exome

AF:

0.692

AC:

205129

AN:

296402

Hom.:

72167

AF XY:

0.699

AC XY:

118102

AN XY:

168850

show subpopulations

African (AFR)

AF:

0.547

AC:

4613

AN:

8436

American (AMR)

AF:

0.822

AC:

21743

AN:

26452

Ashkenazi Jewish (ASJ)

AF:

0.787

AC:

8035

AN:

10216

East Asian (EAS)

AF:

0.930

AC:

8508

AN:

9150

South Asian (SAS)

AF:

0.751

AC:

43409

AN:

57804

European-Finnish (FIN)

AF:

0.563

AC:

7009

AN:

12454

Middle Eastern (MID)

AF:

0.727

AC:

1987

AN:

2734

European-Non Finnish (NFE)

AF:

0.646

AC:

100230

AN:

155232

Other (OTH)

AF:

0.689

AC:

9595

AN:

13924

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

2817

5634

8450

11267

14084

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

598

1196

1794

2392

2990

<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:

0.644

AC:

97947

AN:

152110

Hom.:

32153

Cov.:

AF XY:

0.647

AC XY:

48132

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.547

AC:

22679

AN:

41480

American (AMR)

AF:

0.760

AC:

11616

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.790

AC:

2743

AN:

3472

East Asian (EAS)

AF:

0.924

AC:

4779

AN:

5170

South Asian (SAS)

AF:

0.765

AC:

3694

AN:

4828

European-Finnish (FIN)

AF:

0.557

AC:

5895

AN:

10578

Middle Eastern (MID)

AF:

0.772

AC:

227

AN:

294

European-Non Finnish (NFE)

AF:

0.651

AC:

44229

AN:

67972

Other (OTH)

AF:

0.690

AC:

1458

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1747

3494

5240

6987

8734

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

790

1580

2370

3160

3950

<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:

0.661

Hom.:

43731

Bravo

AF:

0.656

Asia WGS

AF:

0.825

AC:

2869

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.053

(source)

DANN

Benign

0.56

PhyloP100

-1.4

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