rs4947342

Variant names:

• chr6-32685293-G-A
• rs4947342

Your query was ambiguous. Multiple possible variants found:

• chr6-32685293-G-A
• chr6-32685293-G-T

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 0.25 in 151,960 control chromosomes in the GnomAD database, including 5,101 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 0.25 (5101 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 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: 0.250 AC: 38017 AN: 151842 Hom.: 5096 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.250 AC: 38051 AN: 151960 Hom.: 5101 Cov.: 31 AF XY: 0.256 AC XY: 19048 AN XY: 74302

African (AFR) AF: 0.209 AC: 8651 AN: 41438

American (AMR) AF: 0.373 AC: 5692 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1179 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1706 AN: 5146

South Asian (SAS) AF: 0.344 AC: 1658 AN: 4814

European-Finnish (FIN) AF: 0.265 AC: 2793 AN: 10558

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15529 AN: 67964

Other (OTH) AF: 0.266 AC: 560 AN: 2106

Alfa AF: 0.252 Hom.: 14042

Bravo AF: 0.262

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
DANN	Benign	0.80
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4947342; hg19: chr6-32653070;