6-32753003-A-G

Variant names:

• chr6-32753003-A-G
• rs10947342

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 0.499 in 152,044 control chromosomes in the GnomAD database, including 19,790 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 0.50 (19790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.573
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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: 0.498 AC: 75723 AN: 151924 Hom.: 19760 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.499 AC: 75813 AN: 152044 Hom.: 19790 Cov.: 32 AF XY: 0.508 AC XY: 37785 AN XY: 74314

African (AFR) AF: 0.389 AC: 16150 AN: 41468

American (AMR) AF: 0.553 AC: 8445 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1935 AN: 3468

East Asian (EAS) AF: 0.810 AC: 4190 AN: 5174

South Asian (SAS) AF: 0.682 AC: 3286 AN: 4820

European-Finnish (FIN) AF: 0.576 AC: 6079 AN: 10558

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.497 AC: 33801 AN: 67974

Other (OTH) AF: 0.528 AC: 1113 AN: 2108

Alfa AF: 0.496 Hom.: 2511

Bravo AF: 0.491

Asia WGS AF: 0.705 AC: 2445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs10947342; hg19: chr6-32720780;