rs1481980

Positions:

• chr11-103480247-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.684

Alfa AF: 0.751 Hom.: 55646

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1481980; hg19: chr11-103350975;