rs1799724

chr6-31574705-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 0.088 in 151,940 control chromosomes in the GnomAD database, including 838 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.088 (838 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: risk factor no assertion criteria provided O:2
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0879 AC: 13352 AN: 151822 Hom.: 835 Cov.: 31

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.0826

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.0880 AC: 13375 AN: 151940 Hom.: 838 Cov.: 31 AF XY: 0.0898 AC XY: 6666 AN XY: 74258

Gnomad4 AFR AF: 0.0309

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0557

Gnomad4 NFE AF: 0.0940

Gnomad4 OTH AF: 0.103

Alfa AF: 0.121 Hom.: 1422

Bravo AF: 0.0935

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:2

Revision: no assertion criteria provided

Submissions by phenotype

Alzheimer disease, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jul 01, 2005

- -

Vascular dementia, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jul 01, 2005

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.5
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1799724; hg19: chr6-31542482;