rs11935463

Variant names:

• chr4-147255905-T-C
• rs11935463

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 0.909 in 152,274 control chromosomes in the GnomAD database, including 63,001 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 0.91 (63001 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.919 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: 0.909 AC: 138312 AN: 152154 Hom.: 62972 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.909 AC: 138398 AN: 152274 Hom.: 63001 Cov.: 32 AF XY: 0.905 AC XY: 67374 AN XY: 74448

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.925

Gnomad4 OTH AF: 0.894

Alfa AF: 0.919 Hom.: 7996

Bravo AF: 0.909

Asia WGS AF: 0.802 AC: 2789 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	2.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11935463; hg19: chr4-148177057;