6-43768652-A-C

Variant names:

• chr6-43768652-A-C
• rs699947

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.597 in 152,102 control chromosomes in the GnomAD database, including 28,280 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.60 (28280 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 1.03
• Publications: 784 publications found

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 6-43768652-A-C is Benign according to our data. Variant chr6-43768652-A-C is described in ClinVar as Benign. ClinVar VariationId is 12224.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90793 AN: 151984 Hom.: 28251 Cov.: 33

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.597 AC: 90880 AN: 152102 Hom.: 28280 Cov.: 33 AF XY: 0.595 AC XY: 44239 AN XY: 74346

African (AFR) AF: 0.789 AC: 32720 AN: 41482

American (AMR) AF: 0.613 AC: 9374 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1865 AN: 3472

East Asian (EAS) AF: 0.723 AC: 3727 AN: 5152

South Asian (SAS) AF: 0.552 AC: 2665 AN: 4824

European-Finnish (FIN) AF: 0.447 AC: 4727 AN: 10578

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34085 AN: 67980

Other (OTH) AF: 0.616 AC: 1302 AN: 2112

Alfa AF: 0.549 Hom.: 14592

Bravo AF: 0.623

Asia WGS AF: 0.611 AC: 2124 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Atherosclerosis, susceptibility to Benign:1

Dec 01, 2009

OMIM

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.75
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs699947; hg19: chr6-43736389;