chr9-111740462-G-A

Variant names:

• chr9-111740462-G-A
• rs10981043
• NM_001378211.1:c.1174+1014C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378211.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHOC1	NM_001378211.1	MANE Select	c.1174+1014C>T		intron	N/A	NP_001365140.1
	SHOC1	NM_173521.5		c.982+1014C>T		intron	N/A	NP_775792.5
	SHOC1	NM_001080551.3		c.865+1014C>T		intron	N/A	NP_001074020.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHOC1	ENST00000682961.1	MANE Select	c.1174+1014C>T		intron	N/A	ENSP00000508388.1
	SHOC1	ENST00000318737.8	TSL:1	c.982+1014C>T		intron	N/A	ENSP00000322108.4
	SHOC1	ENST00000394777.8	TSL:1	c.865+1014C>T		intron	N/A	ENSP00000378257.4

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

African (AFR) AF: 0.166 AC: 6890 AN: 41472

American (AMR) AF: 0.148 AC: 2267 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3466

East Asian (EAS) AF: 0.0263 AC: 136 AN: 5180

South Asian (SAS) AF: 0.176 AC: 847 AN: 4814

European-Finnish (FIN) AF: 0.201 AC: 2122 AN: 10572

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15214 AN: 67980

Other (OTH) AF: 0.182 AC: 383 AN: 2108

Alfa AF: 0.190 Hom.: 515

Bravo AF: 0.184

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.71
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10981043; hg19: chr9-114502742;