11-124071072-G-T

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 0.585 in 151,724 control chromosomes in the GnomAD database, including 26,420 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 0.59 (26420 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 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: 0.585 AC: 88744 AN: 151606 Hom.: 26403 Cov.: 30

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.585 AC: 88798 AN: 151724 Hom.: 26420 Cov.: 30 AF XY: 0.589 AC XY: 43664 AN XY: 74122

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.571

Alfa AF: 0.547 Hom.: 3202

Bravo AF: 0.570

Asia WGS AF: 0.616 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6590039; hg19: chr11-123941779;