6-32225443-A-G

Variant names:

• chr6-32225443-A-G
• rs2395106

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 0.461 in 151,250 control chromosomes in the GnomAD database, including 16,604 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 0.46 (16604 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69580 AN: 151134 Hom.: 16580 Cov.: 30

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.461 AC: 69660 AN: 151250 Hom.: 16604 Cov.: 30 AF XY: 0.468 AC XY: 34536 AN XY: 73862

African (AFR) AF: 0.541 AC: 22248 AN: 41092

American (AMR) AF: 0.474 AC: 7202 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1810 AN: 3468

East Asian (EAS) AF: 0.650 AC: 3360 AN: 5166

South Asian (SAS) AF: 0.585 AC: 2807 AN: 4800

European-Finnish (FIN) AF: 0.425 AC: 4389 AN: 10320

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26213 AN: 67902

Other (OTH) AF: 0.481 AC: 1012 AN: 2102

Alfa AF: 0.444 Hom.: 5076

Bravo AF: 0.465

Asia WGS AF: 0.621 AC: 2154 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.86
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2395106; hg19: chr6-32193220;