6-32713384-G-T

Variant names:

• chr6-32713384-G-T
• rs2858332

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 0.541 in 152,030 control chromosomes in the GnomAD database, including 22,770 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 (22770 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 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: 0.541 AC: 82197 AN: 151910 Hom.: 22762 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.541 AC: 82254 AN: 152030 Hom.: 22770 Cov.: 32 AF XY: 0.544 AC XY: 40408 AN XY: 74326

African (AFR) AF: 0.544 AC: 22560 AN: 41454

American (AMR) AF: 0.623 AC: 9516 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2426 AN: 3464

East Asian (EAS) AF: 0.714 AC: 3696 AN: 5180

South Asian (SAS) AF: 0.656 AC: 3161 AN: 4822

European-Finnish (FIN) AF: 0.474 AC: 5010 AN: 10566

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33759 AN: 67964

Other (OTH) AF: 0.608 AC: 1277 AN: 2102

Alfa AF: 0.522 Hom.: 38455

Bravo AF: 0.553

Asia WGS AF: 0.697 AC: 2425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.40
DANN	Benign	0.43
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2858332; hg19: chr6-32681161;