6-31574699-C-A

Position:

• chr6-31574699-C-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.144 in 151,842 control chromosomes in the GnomAD database, including 1,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective (no stars).

• Frequency: Genomes: 𝑓 0.14 (1698 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: protective no assertion criteria provided B:1
• Conservation: PhyloP100: -2.77

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 6-31574699-C-A is Benign according to our data. Variant chr6-31574699-C-A is described in ClinVar as [protective]. Clinvar id is 12390.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_benign, oryginal submission is: [protective].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 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: 0.144 AC: 21898 AN: 151724 Hom.: 1699 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.144 AC: 21905 AN: 151842 Hom.: 1698 Cov.: 31 AF XY: 0.146 AC XY: 10802 AN XY: 74186

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.163

Alfa AF: 0.153 Hom.: 2867

Bravo AF: 0.141

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Significance: protective

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Alzheimer disease, protection against Benign:1

protective, no assertion criteria provided

literature only

OMIM

Aug 01, 2006

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.65
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800630; hg19: chr6-31542476;