chr6-132558216-A-G

Variant names:

• chr6-132558216-A-G
• rs2840836

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 0.796 in 152,108 control chromosomes in the GnomAD database, including 48,654 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 0.80 (48654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 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: 0.796 AC: 120985 AN: 151990 Hom.: 48619 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.796 AC: 121076 AN: 152108 Hom.: 48654 Cov.: 32 AF XY: 0.798 AC XY: 59276 AN XY: 74326

African (AFR) AF: 0.902 AC: 37425 AN: 41496

American (AMR) AF: 0.746 AC: 11416 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2630 AN: 3470

East Asian (EAS) AF: 0.885 AC: 4585 AN: 5178

South Asian (SAS) AF: 0.845 AC: 4072 AN: 4818

European-Finnish (FIN) AF: 0.756 AC: 7982 AN: 10560

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50508 AN: 67978

Other (OTH) AF: 0.796 AC: 1677 AN: 2108

Alfa AF: 0.776 Hom.: 5689

Bravo AF: 0.799

Asia WGS AF: 0.864 AC: 3005 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.1
DANN	Benign	0.72
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2840836; hg19: chr6-132879355; COSMIC: COSV51587164;