rs1799724

Variant names:

• chr6-31574705-C-T
• rs1799724

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

Jul 01, 2005

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

VASCULAR DEMENTIA, SUSCEPTIBILITY TO Other:1

Jul 01, 2005

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

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;