6-32252707-C-G

Variant names:

• chr6-32252707-C-G
• rs3115572

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 0.634 in 151,604 control chromosomes in the GnomAD database, including 30,921 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 0.63 (30921 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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: 0.634 AC: 96033 AN: 151486 Hom.: 30896 Cov.: 30

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.634 AC: 96106 AN: 151604 Hom.: 30921 Cov.: 30 AF XY: 0.638 AC XY: 47207 AN XY: 74046

African (AFR) AF: 0.584 AC: 24086 AN: 41242

American (AMR) AF: 0.761 AC: 11592 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2982 AN: 3468

East Asian (EAS) AF: 0.792 AC: 4099 AN: 5178

South Asian (SAS) AF: 0.770 AC: 3706 AN: 4816

European-Finnish (FIN) AF: 0.571 AC: 5973 AN: 10464

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41454 AN: 67902

Other (OTH) AF: 0.688 AC: 1443 AN: 2096

Alfa AF: 0.458 Hom.: 1130

Bravo AF: 0.643

Asia WGS AF: 0.785 AC: 2730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.60
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3115572; hg19: chr6-32220484;