rs10981043

chr9-111740462-G-A

Variant summary

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

The NM_001378211.1(SHOC1):c.1174+1014C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,074 control chromosomes in the GnomAD database, including 2,924 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 0.19 (2924 hom., cov: 33)
• Consequence: SHOC1 NM_001378211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SHOC1	NM_001378211.1	c.1174+1014C>T		intron_variant		ENST00000682961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SHOC1	ENST00000682961.1	c.1174+1014C>T		intron_variant			NM_001378211.1	A2

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28810 AN: 151956 Hom.: 2927 Cov.: 33

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.186

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.189 AC: 28817 AN: 152074 Hom.: 2924 Cov.: 33 AF XY: 0.185 AC XY: 13740 AN XY: 74340

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.0263

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.182

Alfa AF: 0.190 Hom.: 503

Bravo AF: 0.184

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.4
Dann	Benign	0.71

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: rs10981043; hg19: chr9-114502742;