chr6-32692101-A-G

Variant names:

• chr6-32692101-A-G
• rs9275224

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 0.536 in 152,002 control chromosomes in the GnomAD database, including 22,313 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 0.54 (22313 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811
• Publications: 70 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81454 AN: 151884 Hom.: 22292 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.536 AC: 81531 AN: 152002 Hom.: 22313 Cov.: 32 AF XY: 0.541 AC XY: 40194 AN XY: 74300

African (AFR) AF: 0.524 AC: 21710 AN: 41428

American (AMR) AF: 0.634 AC: 9689 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3466

East Asian (EAS) AF: 0.652 AC: 3372 AN: 5170

South Asian (SAS) AF: 0.417 AC: 2006 AN: 4810

European-Finnish (FIN) AF: 0.616 AC: 6523 AN: 10582

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34108 AN: 67954

Other (OTH) AF: 0.554 AC: 1171 AN: 2114

Alfa AF: 0.524 Hom.: 54350

Bravo AF: 0.543

Asia WGS AF: 0.596 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.2
DANN	Benign	0.66
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs9275224; hg19: chr6-32659878;