rs953536

Positions:

• chr9-111727607-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SHOC1	NM_001378211.1	c.1834+26G>A		intron_variant		ENST00000682961.1	NP_001365140.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SHOC1	ENST00000682961.1	c.1834+26G>A		intron_variant			NM_001378211.1	ENSP00000508388	A2

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83500 AN: 151846 Hom.: 23628 Cov.: 32

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

GnomAD3 exomes AF: 0.597 AC: 113130 AN: 189404 Hom.: 34907 AF XY: 0.591 AC XY: 59540 AN XY: 100660

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 SAS exome AF: 0.558

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.: 27 AF XY: 0.556 AC XY: 376503 AN XY: 677374

Gnomad4 AFR exome AF: 0.461

Gnomad4 AMR exome AF: 0.705

Gnomad4 ASJ exome AF: 0.561

Gnomad4 EAS exome AF: 0.892

Gnomad4 SAS exome AF: 0.552

Gnomad4 FIN exome AF: 0.620

Gnomad4 NFE exome AF: 0.540

Gnomad4 OTH exome AF: 0.554

GnomAD4 genome AF: 0.550 AC: 83573 AN: 151964 Hom.: 23649 Cov.: 32 AF XY: 0.560 AC XY: 41575 AN XY: 74278

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.550

Alfa AF: 0.549 Hom.: 40062

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
DANN	Benign	0.54

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

LitVar

Other links and lift over

dbSNP: rs953536; hg19: chr9-114489887;