11-80600627-A-G

Variant names:

• chr11-80600627-A-G
• rs2140930

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 0.54 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.539 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

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.525

Alfa AF: 0.417 Hom.: 14000

Bravo AF: 0.564

Asia WGS AF: 0.787 AC: 2731 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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