chr11-80600627-A-G

Variant names:

• chr11-80600627-A-G
• rs2140930

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 0.54 in 151,938 control chromosomes in the GnomAD database, including 24,995 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 0.54 (24995 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81902 AN: 151820 Hom.: 24932 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.540 AC: 82033 AN: 151938 Hom.: 24995 Cov.: 32 AF XY: 0.546 AC XY: 40563 AN XY: 74260

African (AFR) AF: 0.786 AC: 32584 AN: 41474

American (AMR) AF: 0.590 AC: 8967 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4610 AN: 5142

South Asian (SAS) AF: 0.631 AC: 3041 AN: 4818

European-Finnish (FIN) AF: 0.389 AC: 4115 AN: 10574

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25833 AN: 67952

Other (OTH) AF: 0.525 AC: 1107 AN: 2110

Alfa AF: 0.466 Hom.: 28055

Bravo AF: 0.564

Asia WGS AF: 0.787 AC: 2731 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.72
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2140930; hg19: chr11-80311671; COSMIC: COSV57454167;