rs1799964

Positions:

• chr6-31574531-T-C

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 0.196 in 151,164 control chromosomes in the GnomAD database, including 2,988 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 0.20 (2988 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.311 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: 0.196 AC: 29605 AN: 151046 Hom.: 2988 Cov.: 30

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.196 AC: 29631 AN: 151164 Hom.: 2988 Cov.: 30 AF XY: 0.197 AC XY: 14541 AN XY: 73770

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.236

Alfa AF: 0.211 Hom.: 5947

Bravo AF: 0.194

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1799964; hg19: chr6-31542308;