rs4756763

Variant names:

• chr11-13259009-G-A
• rs4756763
• ENST00000787640.1:n.66-1334G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-13259009-G-A
• chr11-13259009-G-C

Variant summary

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

The ENST00000787640.1(ENSG00000302524):​n.66-1334G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,994 control chromosomes in the GnomAD database, including 18,015 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 0.47 (18015 hom., cov: 31)
• Consequence: ENSG00000302524 ENST00000787640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 11 publications found

Genes affected

ENSG00000302524 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787640.1. 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
	ENSG00000302524	ENST00000787640.1		n.66-1334G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71804 AN: 151876 Hom.: 18002 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.473 AC: 71867 AN: 151994 Hom.: 18015 Cov.: 31 AF XY: 0.470 AC XY: 34921 AN XY: 74264

African (AFR) AF: 0.320 AC: 13254 AN: 41440

American (AMR) AF: 0.486 AC: 7423 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1809 AN: 3468

East Asian (EAS) AF: 0.273 AC: 1405 AN: 5152

South Asian (SAS) AF: 0.454 AC: 2188 AN: 4820

European-Finnish (FIN) AF: 0.522 AC: 5497 AN: 10536

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38775 AN: 67980

Other (OTH) AF: 0.501 AC: 1060 AN: 2116

Alfa AF: 0.555 Hom.: 67277

Bravo AF: 0.465

Asia WGS AF: 0.380 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.30

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: rs4756763;

hg19: chr11-13280556;