11-124071072-G-T

Variant names:

• chr11-124071072-G-T
• rs6590039

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 0.585 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.470 AC: 19407 AN: 41286

American (AMR) AF: 0.580 AC: 8854 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1798 AN: 3466

East Asian (EAS) AF: 0.701 AC: 3608 AN: 5146

South Asian (SAS) AF: 0.595 AC: 2859 AN: 4806

European-Finnish (FIN) AF: 0.701 AC: 7374 AN: 10524

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43009 AN: 67932

Other (OTH) AF: 0.571 AC: 1203 AN: 2106

Alfa AF: 0.543 Hom.: 3290

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
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs6590039; hg19: chr11-123941779;