rs315711

chr9-111786171-G-Achr9-111786171-G-C

Variant summary

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

The NM_001378211.1(SHOC1):c.46-136C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 591,180 control chromosomes in the GnomAD database, including 97,825 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 0.56 (24523 hom., cov: 33)
  • Exomes 𝑓: 0.57 (73302 hom.)
• Consequence: SHOC1 NM_001378211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

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=-0.92).
• 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	UniProt
SHOC1	NM_001378211.1	c.46-136C>T		intron_variant		ENST00000682961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SHOC1	ENST00000682961.1	c.46-136C>T		intron_variant			NM_001378211.1	A2
SHOC1	ENST00000374283.5	c.46-136C>T		intron_variant		1		P4
SHOC1	ENST00000683944.1	c.46-136C>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85136 AN: 151904 Hom.: 24491 Cov.: 33

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.557

GnomAD4 exome AF: 0.568 AC: 249618 AN: 439158 Hom.: 73302 AF XY: 0.568 AC XY: 126701 AN XY: 222902

Gnomad4 AFR exome AF: 0.481

Gnomad4 AMR exome AF: 0.707

Gnomad4 ASJ exome AF: 0.562

Gnomad4 EAS exome AF: 0.904

Gnomad4 SAS exome AF: 0.542

Gnomad4 FIN exome AF: 0.616

Gnomad4 NFE exome AF: 0.544

Gnomad4 OTH exome AF: 0.563

GnomAD4 genome AF: 0.561 AC: 85220 AN: 152022 Hom.: 24523 Cov.: 33 AF XY: 0.570 AC XY: 42395 AN XY: 74314

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.557

Alfa AF: 0.571 Hom.: 8424

Bravo AF: 0.563

Asia WGS AF: 0.689 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.5
Dann	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs315711; hg19: chr9-114548451;