rs879825

Variant names:

• chr6-43796077-A-G
• rs879825

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 0.135 in 152,202 control chromosomes in the GnomAD database, including 1,816 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 0.14 (1816 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 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: 0.135 AC: 20561 AN: 152084 Hom.: 1810 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0889

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0827

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0822

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.135 AC: 20585 AN: 152202 Hom.: 1816 Cov.: 33 AF XY: 0.135 AC XY: 10079 AN XY: 74420

African (AFR) AF: 0.249 AC: 10328 AN: 41492

American (AMR) AF: 0.0887 AC: 1357 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1055 AN: 5176

South Asian (SAS) AF: 0.145 AC: 700 AN: 4826

European-Finnish (FIN) AF: 0.0827 AC: 877 AN: 10604

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0822 AC: 5591 AN: 68016

Other (OTH) AF: 0.140 AC: 295 AN: 2112

Alfa AF: 0.0986 Hom.: 1336

Bravo AF: 0.140

Asia WGS AF: 0.185 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.20
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs879825; hg19: chr6-43763814;