rs1476202

Variant names:

• chr11-123945507-T-C
• rs1476202

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 0.805 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.823 AC: 34194 AN: 41544

American (AMR) AF: 0.854 AC: 13059 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2924 AN: 3472

East Asian (EAS) AF: 0.785 AC: 4062 AN: 5172

South Asian (SAS) AF: 0.699 AC: 3371 AN: 4822

European-Finnish (FIN) AF: 0.836 AC: 8859 AN: 10598

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53462 AN: 68000

Other (OTH) AF: 0.795 AC: 1680 AN: 2114

Alfa AF: 0.786 Hom.: 21440

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1476202; hg19: chr11-123816214;