6-32730008-C-G

Variant names:

• chr6-32730008-C-G
• rs2859113

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 0.505 in 151,824 control chromosomes in the GnomAD database, including 20,498 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 0.51 (20498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 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: 0.505 AC: 76683 AN: 151706 Hom.: 20481 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.505 AC: 76741 AN: 151824 Hom.: 20498 Cov.: 32 AF XY: 0.512 AC XY: 38006 AN XY: 74184

African (AFR) AF: 0.330 AC: 13685 AN: 41408

American (AMR) AF: 0.588 AC: 8964 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1843 AN: 3466

East Asian (EAS) AF: 0.711 AC: 3659 AN: 5148

South Asian (SAS) AF: 0.667 AC: 3217 AN: 4822

European-Finnish (FIN) AF: 0.581 AC: 6113 AN: 10528

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.549 AC: 37282 AN: 67904

Other (OTH) AF: 0.542 AC: 1141 AN: 2106

Alfa AF: 0.388 Hom.: 1111

Bravo AF: 0.501

Asia WGS AF: 0.669 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.53
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2859113; hg19: chr6-32697785; COSMIC: COSV70889578;