rs6929774

Variant names:

• chr6-33594943-C-T
• rs6929774

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.398

Alfa AF: 0.457 Hom.: 32658

Bravo AF: 0.445

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6929774; hg19: chr6-33562720;