rs11265352

Variant names:

• chr1-160189300-A-G
• rs11265352
• ENST00000799012.1:n.268-176T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-160189300-A-G
• chr1-160189300-A-T

Variant summary

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

The ENST00000799012.1(ENSG00000304031):​n.268-176T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,782 control chromosomes in the GnomAD database, including 23,593 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 0.52 (23593 hom., cov: 31)
• Consequence: ENSG00000304031 ENST00000799012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 6 publications found

Genes affected

ENSG00000304031 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 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
ENSG00000304031	ENST00000799012.1	n.268-176T>C		intron_variant	Intron 2 of 3
ENSG00000304031	ENST00000799013.1	n.70+3839T>C		intron_variant	Intron 1 of 1
ENSG00000304031	ENST00000799014.1	n.307-176T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79185 AN: 151664 Hom.: 23584 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.522 AC: 79202 AN: 151782 Hom.: 23593 Cov.: 31 AF XY: 0.531 AC XY: 39381 AN XY: 74162

African (AFR) AF: 0.209 AC: 8661 AN: 41444

American (AMR) AF: 0.670 AC: 10222 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2256 AN: 3464

East Asian (EAS) AF: 0.702 AC: 3617 AN: 5152

South Asian (SAS) AF: 0.642 AC: 3084 AN: 4802

European-Finnish (FIN) AF: 0.672 AC: 7068 AN: 10520

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42390 AN: 67826

Other (OTH) AF: 0.560 AC: 1182 AN: 2110

Alfa AF: 0.599 Hom.: 51079

Bravo AF: 0.509

Asia WGS AF: 0.624 AC: 2171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.028
DANN	Benign	0.73
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs11265352; hg19: chr1-160159090;