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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730456.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295491	ENST00000730456.1		n.89+274A>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10937751;

hg19: chr4-6712056;