rs1892953

Variant names:

• chr11-76561498-G-A
• rs1892953
• ENST00000830356.1:n.399-5853C>T

Variant summary

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

The ENST00000830356.1(ENSG00000308001):​n.399-5853C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,966 control chromosomes in the GnomAD database, including 24,345 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 0.56 (24345 hom., cov: 32)
• Consequence: ENSG00000308001 ENST00000830356.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 11 publications found

Genes affected

ENSG00000308001 (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 (NFE) allele frequency at 95% confidence interval = 0.58 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
ENSG00000308001	ENST00000830356.1	n.399-5853C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85640 AN: 151848 Hom.: 24342 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.564 AC: 85680 AN: 151966 Hom.: 24345 Cov.: 32 AF XY: 0.560 AC XY: 41615 AN XY: 74280

African (AFR) AF: 0.551 AC: 22842 AN: 41422

American (AMR) AF: 0.502 AC: 7663 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2396 AN: 3470

East Asian (EAS) AF: 0.502 AC: 2591 AN: 5160

South Asian (SAS) AF: 0.498 AC: 2394 AN: 4812

European-Finnish (FIN) AF: 0.574 AC: 6069 AN: 10564

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39716 AN: 67966

Other (OTH) AF: 0.571 AC: 1203 AN: 2108

Alfa AF: 0.577 Hom.: 14103

Bravo AF: 0.561

Asia WGS AF: 0.476 AC: 1656 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	0.91
DANN	Benign	0.53
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1892953; hg19: chr11-76272542;