rs10488676

Variant names:

• chr11-5247567-G-A
• rs10488676
• ENST00000759251.1:n.141C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-5247567-G-A
• chr11-5247567-G-C
• chr11-5247567-G-T

Variant summary

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

The ENST00000759251.1(ENSG00000290652):​n.141C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,954 control chromosomes in the GnomAD database, including 15,762 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 0.43 (15762 hom., cov: 32)
• Consequence: ENSG00000290652 ENST00000759251.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 6 publications found

Genes affected

ENSG00000290652 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759251.1. 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
	ENSG00000290652	ENST00000759251.1		n.141C>T		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000290652	ENST00000759252.1		n.88C>T		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000290652	ENST00000759253.1		n.-210C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65447 AN: 151836 Hom.: 15748 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.431 AC: 65498 AN: 151954 Hom.: 15762 Cov.: 32 AF XY: 0.438 AC XY: 32492 AN XY: 74266

African (AFR) AF: 0.225 AC: 9319 AN: 41448

American (AMR) AF: 0.575 AC: 8771 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2241 AN: 3464

East Asian (EAS) AF: 0.775 AC: 3992 AN: 5150

South Asian (SAS) AF: 0.540 AC: 2597 AN: 4808

European-Finnish (FIN) AF: 0.461 AC: 4872 AN: 10558

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.471 AC: 32010 AN: 67954

Other (OTH) AF: 0.494 AC: 1042 AN: 2108

Alfa AF: 0.467 Hom.: 48995

Bravo AF: 0.429

Asia WGS AF: 0.593 AC: 2061 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.54
DANN	Benign	0.46
PhyloP100		-0.24

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: rs10488676;

hg19: chr11-5268797;