dbSNP rs953536: SHOC1:c.1834+26G>A (chr9-111727607-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001378211.1(SHOC1):c.1834+26G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 1,527,950 control chromosomes in the GnomAD database, including 240,076 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 0.55 ( 23649 hom., cov: 32)

Exomes 𝑓: 0.56 ( 216427 hom. )

Consequence

SHOC1
NM_001378211.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.703

Publications

9 publications found

Variant links:

Genes affected

SHOC1 (HGNC:26535): (shortage in chiasmata 1) Enables single-stranded DNA binding activity. Predicted to be involved in resolution of meiotic recombination intermediates. Predicted to be located in chromosome. Predicted to be active in condensed nuclear chromosome. [provided by Alliance of Genome Resources, Apr 2022]

SHOC1 Gene-Disease associations (from GenCC):

spermatogenic failure
Inheritance: AR Classification: LIMITED Submitted by: Franklin by Genoox

SHOC1 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHOC1	NM_001378211.1 link	c.1834+26G>A		intron_variant	Intron 13 of 27	ENST00000682961.1	NP_001365140.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHOC1	ENST00000682961.1 link	c.1834+26G>A		intron_variant	Intron 13 of 27		NM_001378211.1	ENSP00000508388.1		A0A804HLJ8

Frequencies

GnomAD3 genomes

AF:

0.550

AC:

83500

AN:

151846

Hom.:

23628

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.600

Gnomad AMR

AF:

0.642

Gnomad ASJ

AF:

0.547

Gnomad EAS

AF:

0.870

Gnomad SAS

AF:

0.563

Gnomad FIN

AF:

0.632

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.546

Gnomad OTH

AF:

0.550

GnomAD2 exomes

AF:

0.597

AC:

113130

AN:

189404

AF XY:

0.591

show subpopulations

Gnomad AFR exome

AF:

0.458

Gnomad AMR exome

AF:

0.723

Gnomad ASJ exome

AF:

0.550

Gnomad EAS exome

AF:

0.872

Gnomad FIN exome

AF:

0.623

Gnomad NFE exome

AF:

0.548

Gnomad OTH exome

AF:

0.578

GnomAD4 exome

AF:

0.556

AC:

765111

AN:

1375986

Hom.:

216427

Cov.:

AF XY:

0.556

AC XY:

376503

AN XY:

677374

show subpopulations

African (AFR)

AF:

0.461

AC:

14090

AN:

30562

American (AMR)

AF:

0.705

AC:

22026

AN:

31242

Ashkenazi Jewish (ASJ)

AF:

0.561

AC:

11977

AN:

21344

East Asian (EAS)

AF:

0.892

AC:

34578

AN:

38776

South Asian (SAS)

AF:

0.552

AC:

37886

AN:

68650

European-Finnish (FIN)

AF:

0.620

AC:

31025

AN:

50076

Middle Eastern (MID)

AF:

0.554

AC:

2964

AN:

5350

European-Non Finnish (NFE)

AF:

0.540

AC:

579070

AN:

1073102

Other (OTH)

AF:

0.554

AC:

31495

AN:

56884

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

15469

30939

46408

61878

77347

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16880

33760

50640

67520

84400

<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:

0.550

AC:

83573

AN:

151964

Hom.:

23649

Cov.:

AF XY:

0.560

AC XY:

41575

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.460

AC:

19049

AN:

41434

American (AMR)

AF:

0.642

AC:

9798

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.547

AC:

1897

AN:

3466

East Asian (EAS)

AF:

0.870

AC:

4503

AN:

5176

South Asian (SAS)

AF:

0.562

AC:

2714

AN:

4826

European-Finnish (FIN)

AF:

0.632

AC:

6680

AN:

10566

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.546

AC:

37060

AN:

67920

Other (OTH)

AF:

0.550

AC:

1160

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1884

3768

5653

7537

9421

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

724

1448

2172

2896

3620

<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:

0.546

Hom.:

63754

Bravo

AF:

0.549

Asia WGS

AF:

0.679

AC:

2360

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.2

(source)

DANN

Benign

0.54

PhyloP100

-0.70

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over