rs3094572

chr6-29513216-T-C

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 0.635 in 152,110 control chromosomes in the GnomAD database, including 30,929 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 (30929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.762 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: 0.635 AC: 96447 AN: 151992 Hom.: 30883 Cov.: 32

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.635 AC: 96550 AN: 152110 Hom.: 30929 Cov.: 32 AF XY: 0.638 AC XY: 47436 AN XY: 74350

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.609

Alfa AF: 0.608 Hom.: 44379

Bravo AF: 0.629

Asia WGS AF: 0.769 AC: 2675 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	2.0
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094572; hg19: chr6-29480993;