6-30569829-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;