6-105987394-G-C

Variant names:

• chr6-105987394-G-C
• rs7746082

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 0.196 in 152,132 control chromosomes in the GnomAD database, including 3,823 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 0.20 (3823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 64 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29865 AN: 152014 Hom.: 3820 Cov.: 32

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.196 AC: 29865 AN: 152132 Hom.: 3823 Cov.: 32 AF XY: 0.193 AC XY: 14349 AN XY: 74364

African (AFR) AF: 0.0491 AC: 2038 AN: 41524

American (AMR) AF: 0.184 AC: 2809 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5188

South Asian (SAS) AF: 0.158 AC: 760 AN: 4824

European-Finnish (FIN) AF: 0.263 AC: 2773 AN: 10558

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19574 AN: 67968

Other (OTH) AF: 0.219 AC: 461 AN: 2106

Alfa AF: 0.243 Hom.: 2765

Bravo AF: 0.185

Asia WGS AF: 0.0750 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.73
DANN	Benign	0.59
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7746082; hg19: chr6-106435269;