6-32691805-A-G

Variant names:

• chr6-32691805-A-G
• rs4713586

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0542 in 152,182 control chromosomes in the GnomAD database, including 321 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 0.054 (321 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.906
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0921 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0541 AC: 8224 AN: 152064 Hom.: 320 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.0129

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0288

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0542 AC: 8242 AN: 152182 Hom.: 321 Cov.: 32 AF XY: 0.0583 AC XY: 4341 AN XY: 74410

African (AFR) AF: 0.0696 AC: 2891 AN: 41516

American (AMR) AF: 0.0962 AC: 1470 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.0883 AC: 458 AN: 5188

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4820

European-Finnish (FIN) AF: 0.113 AC: 1195 AN: 10592

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0288 AC: 1957 AN: 67996

Other (OTH) AF: 0.0478 AC: 101 AN: 2112

Alfa AF: 0.0568 Hom.: 222

Bravo AF: 0.0561

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.84
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs4713586; hg19: chr6-32659582;