rs11935463

Positions:

• chr4-147255905-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 0.909 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;