11-50138246-T-C

Position:

• chr11-50138246-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 0.463 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.526

Alfa AF: 0.541 Hom.: 32120

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332434; hg19: chr11-50097417;