11-50138246-T-C

Variant names:

• chr11-50138246-T-C
• rs9332434

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 0.463 in 151,968 control chromosomes in the GnomAD database, including 17,905 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 0.46 (17905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.585 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: 0.463 AC: 70318 AN: 151850 Hom.: 17892 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.463 AC: 70342 AN: 151968 Hom.: 17905 Cov.: 32 AF XY: 0.466 AC XY: 34603 AN XY: 74264

African (AFR) AF: 0.239 AC: 9921 AN: 41464

American (AMR) AF: 0.595 AC: 9086 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2299 AN: 3472

East Asian (EAS) AF: 0.535 AC: 2757 AN: 5150

South Asian (SAS) AF: 0.500 AC: 2402 AN: 4802

European-Finnish (FIN) AF: 0.540 AC: 5691 AN: 10544

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36301 AN: 67950

Other (OTH) AF: 0.526 AC: 1111 AN: 2112

Alfa AF: 0.518 Hom.: 51961

Bravo AF: 0.461

Asia WGS AF: 0.476 AC: 1655 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	0.17
DANN	Benign	0.41
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9332434; hg19: chr11-50097417;