rs4930046

chr11-2175918-G-Achr11-2175918-G-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 0.401 in 151,944 control chromosomes in the GnomAD database, including 14,280 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 0.40 (14280 hom., cov: 36)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.83

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 (EAS) allele frequency at 95% confidence interval = 0.767 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: 0.402 AC: 60991 AN: 151826 Hom.: 14284 Cov.: 36

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.401 AC: 60986 AN: 151944 Hom.: 14280 Cov.: 36 AF XY: 0.411 AC XY: 30541 AN XY: 74242

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.460

Alfa AF: 0.421 Hom.: 1813

Bravo AF: 0.385

Asia WGS AF: 0.673 AC: 2342 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	0.35
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4930046; hg19: chr11-2197148;