rs6929774

Positions:

• chr6-33594943-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;