rs10937751

Variant names:

• chr4-6710329-A-C
• rs10937751
• ENST00000730456.1:n.89+274A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000730456.1(ENSG00000295491):​n.89+274A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 151,986 control chromosomes in the GnomAD database, including 40,726 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 0.73 (40726 hom., cov: 31)
• Consequence: ENSG00000295491 ENST00000730456.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 9 publications found

Genes affected

ENSG00000295491 (HGNC:58724):

LOC105378240 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378240	XR_001741568.3	n.121+274A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295491	ENST00000730456.1	n.89+274A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.731 AC: 110995 AN: 151868 Hom.: 40696 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.731 AC: 111080 AN: 151986 Hom.: 40726 Cov.: 31 AF XY: 0.732 AC XY: 54372 AN XY: 74280

African (AFR) AF: 0.746 AC: 30916 AN: 41426

American (AMR) AF: 0.777 AC: 11880 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2425 AN: 3468

East Asian (EAS) AF: 0.598 AC: 3082 AN: 5154

South Asian (SAS) AF: 0.634 AC: 3052 AN: 4812

European-Finnish (FIN) AF: 0.798 AC: 8419 AN: 10552

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48843 AN: 67974

Other (OTH) AF: 0.723 AC: 1526 AN: 2110

Alfa AF: 0.720 Hom.: 30583

Bravo AF: 0.730

Asia WGS AF: 0.611 AC: 2122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		-0.78
PromoterAI		-0.00090	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10937751; hg19: chr4-6712056;