chr11-79976944-G-A

Variant names:

• chr11-79976944-G-A
• rs672600

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 0.485 in 152,004 control chromosomes in the GnomAD database, including 18,839 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 0.49 (18839 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 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: 0.485 AC: 73681 AN: 151888 Hom.: 18816 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.485 AC: 73761 AN: 152004 Hom.: 18839 Cov.: 33 AF XY: 0.499 AC XY: 37065 AN XY: 74288

African (AFR) AF: 0.371 AC: 15389 AN: 41436

American (AMR) AF: 0.564 AC: 8613 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3470

East Asian (EAS) AF: 0.850 AC: 4389 AN: 5166

South Asian (SAS) AF: 0.562 AC: 2706 AN: 4812

European-Finnish (FIN) AF: 0.636 AC: 6725 AN: 10574

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32887 AN: 67952

Other (OTH) AF: 0.465 AC: 983 AN: 2112

Alfa AF: 0.358 Hom.: 1023

Bravo AF: 0.478

Asia WGS AF: 0.679 AC: 2357 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.48
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs672600; hg19: chr11-79687987;