rs6933763

Positions:

• chr6-32755075-A-G

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 0.117 in 152,028 control chromosomes in the GnomAD database, including 1,272 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 0.12 (1272 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.175 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: 0.117 AC: 17740 AN: 151910 Hom.: 1262 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0910

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0387

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.117 AC: 17788 AN: 152028 Hom.: 1272 Cov.: 31 AF XY: 0.117 AC XY: 8727 AN XY: 74336

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0916

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.0387

Gnomad4 NFE AF: 0.0869

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0978 Hom.: 153

Bravo AF: 0.123

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.1
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6933763; hg19: chr6-32722852;