6-30094133-G-A

Variant names:

• chr6-30094133-G-A
• rs17194174

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 0.235 in 152,132 control chromosomes in the GnomAD database, including 5,453 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 0.23 (5453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 10 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 = 0.419 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: 0.235 AC: 35658 AN: 152014 Hom.: 5445 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.235 AC: 35691 AN: 152132 Hom.: 5453 Cov.: 32 AF XY: 0.230 AC XY: 17104 AN XY: 74388

African (AFR) AF: 0.424 AC: 17583 AN: 41446

American (AMR) AF: 0.227 AC: 3469 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3470

East Asian (EAS) AF: 0.163 AC: 846 AN: 5182

South Asian (SAS) AF: 0.294 AC: 1413 AN: 4814

European-Finnish (FIN) AF: 0.0507 AC: 538 AN: 10614

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10320 AN: 68010

Other (OTH) AF: 0.266 AC: 561 AN: 2112

Alfa AF: 0.195 Hom.: 5948

Bravo AF: 0.261

Asia WGS AF: 0.245 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.58
DANN	Benign	0.32
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs17194174; hg19: chr6-30061910;