rs1481980

Variant names:

• chr11-103480247-C-T
• rs1481980

Variant summary

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

The variant allele was found at a frequency of 0.662 in 151,904 control chromosomes in the GnomAD database, including 34,487 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 0.66 (34487 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 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

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100533 AN: 151786 Hom.: 34460 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.662 AC: 100597 AN: 151904 Hom.: 34487 Cov.: 31 AF XY: 0.661 AC XY: 49034 AN XY: 74228

African (AFR) AF: 0.502 AC: 20799 AN: 41406

American (AMR) AF: 0.690 AC: 10528 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2765 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2190 AN: 5156

South Asian (SAS) AF: 0.644 AC: 3092 AN: 4798

European-Finnish (FIN) AF: 0.695 AC: 7317 AN: 10530

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51589 AN: 67966

Other (OTH) AF: 0.684 AC: 1441 AN: 2106

Alfa AF: 0.747 Hom.: 65049

Bravo AF: 0.652

Asia WGS AF: 0.546 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.49
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs1481980; hg19: chr11-103350975;