6-30569829-C-G

Variant names:

• chr6-30569829-C-G
• rs3132613

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.727 in 152,164 control chromosomes in the GnomAD database, including 40,607 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 0.73 (40607 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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: 0.727 AC: 110521 AN: 152046 Hom.: 40562 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.727 AC: 110624 AN: 152164 Hom.: 40607 Cov.: 33 AF XY: 0.724 AC XY: 53853 AN XY: 74376

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.820

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.727

Alfa AF: 0.686 Hom.: 17594

Bravo AF: 0.730

Asia WGS AF: 0.779 AC: 2710 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	1.2
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132613; hg19: chr6-30537606;