rs1481963

Positions:

• chr11-103523199-G-A
• chr11-103523199-G-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 0.603 in 151,220 control chromosomes in the GnomAD database, including 29,433 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 0.60 (29433 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.103523199G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91105 AN: 151104 Hom.: 29431 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.603 AC: 91129 AN: 151220 Hom.: 29433 Cov.: 32 AF XY: 0.606 AC XY: 44777 AN XY: 73924

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.638

Alfa AF: 0.641 Hom.: 5357

Bravo AF: 0.592

Asia WGS AF: 0.663 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1481963; hg19: chr11-103393927;