6-32710820-C-G

Variant names:

• chr6-32710820-C-G
• rs4273729

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 0.59 in 151,866 control chromosomes in the GnomAD database, including 26,809 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 0.59 (26809 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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: 0.590 AC: 89553 AN: 151748 Hom.: 26802 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.590 AC: 89608 AN: 151866 Hom.: 26809 Cov.: 32 AF XY: 0.590 AC XY: 43813 AN XY: 74204

African (AFR) AF: 0.562 AC: 23282 AN: 41436

American (AMR) AF: 0.643 AC: 9823 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2616 AN: 3468

East Asian (EAS) AF: 0.730 AC: 3766 AN: 5162

South Asian (SAS) AF: 0.667 AC: 3212 AN: 4812

European-Finnish (FIN) AF: 0.544 AC: 5721 AN: 10526

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38969 AN: 67870

Other (OTH) AF: 0.641 AC: 1354 AN: 2112

Alfa AF: 0.567 Hom.: 2935

Bravo AF: 0.599

Asia WGS AF: 0.716 AC: 2486 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.36
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs4273729; hg19: chr6-32678597;