rs4902762

Variant names:

• chr14-39545301-A-G
• rs4902762
• ENST00000650911.1:n.112+74901A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-39545301-A-G
• chr14-39545301-A-T

Variant summary

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

The ENST00000650911.1(ENSG00000258526):​n.112+74901A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,164 control chromosomes in the GnomAD database, including 53,200 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 0.84 (53200 hom., cov: 32)
• Consequence: ENSG00000258526 ENST00000650911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 5 publications found

Genes affected

ENSG00000258526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650911.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258526	ENST00000650911.1		n.112+74901A>G		intron	N/A
	ENSG00000258526	ENST00000651829.1		n.566+12448A>G		intron	N/A
	ENSG00000258526	ENST00000652126.1		n.152+74901A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126988 AN: 152046 Hom.: 53157 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.835 AC: 127085 AN: 152164 Hom.: 53200 Cov.: 32 AF XY: 0.835 AC XY: 62145 AN XY: 74386

African (AFR) AF: 0.786 AC: 32602 AN: 41500

American (AMR) AF: 0.874 AC: 13354 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2849 AN: 3466

East Asian (EAS) AF: 0.925 AC: 4794 AN: 5182

South Asian (SAS) AF: 0.872 AC: 4210 AN: 4828

European-Finnish (FIN) AF: 0.839 AC: 8885 AN: 10586

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57733 AN: 68010

Other (OTH) AF: 0.828 AC: 1747 AN: 2110

Alfa AF: 0.846 Hom.: 24467

Bravo AF: 0.837

Asia WGS AF: 0.896 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.86
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4902762; hg19: chr14-40014505;