6-138128932-A-G

Variant names:

• chr6-138128932-A-G
• rs6920846

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 0.336 in 151,914 control chromosomes in the GnomAD database, including 9,281 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 0.34 (9281 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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: 0.336 AC: 50984 AN: 151798 Hom.: 9253 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.336 AC: 51052 AN: 151914 Hom.: 9281 Cov.: 31 AF XY: 0.338 AC XY: 25084 AN XY: 74234

African (AFR) AF: 0.255 AC: 10560 AN: 41422

American (AMR) AF: 0.386 AC: 5900 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1203 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3744 AN: 5142

South Asian (SAS) AF: 0.469 AC: 2246 AN: 4794

European-Finnish (FIN) AF: 0.290 AC: 3063 AN: 10564

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.343 AC: 23283 AN: 67938

Other (OTH) AF: 0.345 AC: 728 AN: 2108

Alfa AF: 0.342 Hom.: 36598

Bravo AF: 0.339

Asia WGS AF: 0.567 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.6
DANN	Benign	0.62
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs6920846; hg19: chr6-138450069;