rs6929774

Variant names:

• chr6-33594943-C-T
• rs6929774

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 0.446 in 151,894 control chromosomes in the GnomAD database, including 15,194 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 0.45 (15194 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 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: 0.446 AC: 67698 AN: 151774 Hom.: 15184 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.446 AC: 67739 AN: 151894 Hom.: 15194 Cov.: 31 AF XY: 0.447 AC XY: 33152 AN XY: 74224

African (AFR) AF: 0.412 AC: 17081 AN: 41422

American (AMR) AF: 0.468 AC: 7136 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3470

East Asian (EAS) AF: 0.394 AC: 2026 AN: 5146

South Asian (SAS) AF: 0.474 AC: 2282 AN: 4814

European-Finnish (FIN) AF: 0.465 AC: 4895 AN: 10524

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31237 AN: 67950

Other (OTH) AF: 0.398 AC: 839 AN: 2106

Alfa AF: 0.455 Hom.: 50556

Bravo AF: 0.445

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.63
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6929774; hg19: chr6-33562720;