rs1476202

Positions:

• chr11-123945507-T-C

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 0.805 in 152,222 control chromosomes in the GnomAD database, including 49,480 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 0.81 (49480 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

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 (AMR) allele frequency at 95% confidence interval = 0.841 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: 0.805 AC: 122498 AN: 152104 Hom.: 49430 Cov.: 34

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.805 AC: 122601 AN: 152222 Hom.: 49480 Cov.: 34 AF XY: 0.807 AC XY: 60058 AN XY: 74424

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.795

Alfa AF: 0.785 Hom.: 18725

Bravo AF: 0.811

Asia WGS AF: 0.737 AC: 2563 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	0.15
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476202; hg19: chr11-123816214;