6-32712345-G-A

Variant names:

• chr6-32712345-G-A
• rs3135461

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 0.77 in 151,498 control chromosomes in the GnomAD database, including 45,107 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 0.77 (45107 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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: 0.770 AC: 116531 AN: 151380 Hom.: 45066 Cov.: 30

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.770 AC: 116629 AN: 151498 Hom.: 45107 Cov.: 30 AF XY: 0.770 AC XY: 57010 AN XY: 74052

African (AFR) AF: 0.732 AC: 30219 AN: 41260

American (AMR) AF: 0.809 AC: 12315 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2924 AN: 3462

East Asian (EAS) AF: 0.872 AC: 4503 AN: 5164

South Asian (SAS) AF: 0.778 AC: 3739 AN: 4806

European-Finnish (FIN) AF: 0.785 AC: 8284 AN: 10552

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 51944 AN: 67722

Other (OTH) AF: 0.796 AC: 1669 AN: 2098

Alfa AF: 0.785 Hom.: 48612

Bravo AF: 0.775

Asia WGS AF: 0.855 AC: 2976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.34
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3135461; hg19: chr6-32680122;