rs10501267

Variant names:

• chr11-41511059-G-A
• rs10501267
• ENST00000816184.1:n.249+25954G>A

Variant summary

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

The ENST00000816184.1(ENSG00000306191):​n.249+25954G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0825 in 152,100 control chromosomes in the GnomAD database, including 644 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 0.083 (644 hom., cov: 32)
• Consequence: ENSG00000306191 ENST00000816184.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 4 publications found

Genes affected

ENSG00000306191 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816184.1. 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
	ENSG00000306191	ENST00000816184.1		n.249+25954G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0826 AC: 12550 AN: 151984 Hom.: 643 Cov.: 32

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.0728

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0825 AC: 12554 AN: 152100 Hom.: 644 Cov.: 32 AF XY: 0.0813 AC XY: 6045 AN XY: 74356

African (AFR) AF: 0.0240 AC: 996 AN: 41524

American (AMR) AF: 0.0948 AC: 1447 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3472

East Asian (EAS) AF: 0.0465 AC: 240 AN: 5164

South Asian (SAS) AF: 0.0989 AC: 477 AN: 4822

European-Finnish (FIN) AF: 0.0728 AC: 770 AN: 10580

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7897 AN: 67968

Other (OTH) AF: 0.0901 AC: 190 AN: 2108

Alfa AF: 0.108 Hom.: 3122

Bravo AF: 0.0820

Asia WGS AF: 0.0750 AC: 258 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.29
DANN	Benign	0.19
PhyloP100		-0.71

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: rs10501267;

hg19: chr11-41532609;

COSMIC: COSV56523531;