chr6-32787513-T-C

Variant names:

• chr6-32787513-T-C
• rs7762279

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 0.0817 in 152,178 control chromosomes in the GnomAD database, including 584 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 0.082 (584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0817 AC: 12424 AN: 152060 Hom.: 584 Cov.: 32

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0817 AC: 12426 AN: 152178 Hom.: 584 Cov.: 32 AF XY: 0.0777 AC XY: 5780 AN XY: 74372

African (AFR) AF: 0.0850 AC: 3528 AN: 41504

American (AMR) AF: 0.0506 AC: 773 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0591 AC: 205 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.000829 AC: 4 AN: 4826

European-Finnish (FIN) AF: 0.0813 AC: 860 AN: 10578

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6850 AN: 67996

Other (OTH) AF: 0.0681 AC: 144 AN: 2116

Alfa AF: 0.106 Hom.: 1597

Bravo AF: 0.0792

Asia WGS AF: 0.00752 AC: 28 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.3
DANN	Benign	0.50
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7762279; hg19: chr6-32755290;