rs11209261

Variant names:

• chr1-68319530-T-A
• rs11209261
• ENST00000723549.1:n.400-11485T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-68319530-T-A
• chr1-68319530-T-G

Variant summary

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

The ENST00000723549.1(ENSG00000294429):​n.400-11485T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,102 control chromosomes in the GnomAD database, including 40,407 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 (40407 hom., cov: 32)
• Consequence: ENSG00000294429 ENST00000723549.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 3 publications found

Genes affected

ENSG00000294429 (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 (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294429	ENST00000723549.1	n.400-11485T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110217 AN: 151984 Hom.: 40384 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.725 AC: 110284 AN: 152102 Hom.: 40407 Cov.: 32 AF XY: 0.718 AC XY: 53379 AN XY: 74346

African (AFR) AF: 0.770 AC: 31939 AN: 41484

American (AMR) AF: 0.562 AC: 8587 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2953 AN: 3472

East Asian (EAS) AF: 0.763 AC: 3953 AN: 5180

South Asian (SAS) AF: 0.727 AC: 3501 AN: 4818

European-Finnish (FIN) AF: 0.645 AC: 6817 AN: 10574

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.738 AC: 50191 AN: 67988

Other (OTH) AF: 0.715 AC: 1510 AN: 2112

Alfa AF: 0.721 Hom.: 4940

Bravo AF: 0.719

Asia WGS AF: 0.733 AC: 2547 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11209261; hg19: chr1-68785213; COSMIC: COSV59952130;