rs11935463

Variant names:

• chr4-147255905-T-C
• rs11935463

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 0.909 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.912 AC: 37878 AN: 41544

American (AMR) AF: 0.909 AC: 13902 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3072 AN: 3472

East Asian (EAS) AF: 0.776 AC: 4011 AN: 5166

South Asian (SAS) AF: 0.817 AC: 3944 AN: 4826

European-Finnish (FIN) AF: 0.912 AC: 9687 AN: 10618

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.925 AC: 62930 AN: 68030

Other (OTH) AF: 0.894 AC: 1892 AN: 2116

Alfa AF: 0.919 Hom.: 8335

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11935463; hg19: chr4-148177057;