rs3094061

chr6-30353412-A-Cchr6-30353412-A-T

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 0.106 in 152,228 control chromosomes in the GnomAD database, including 973 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 0.11 (973 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.629

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 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: 0.106 AC: 16145 AN: 152110 Hom.: 972 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0509

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0762

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.106 AC: 16148 AN: 152228 Hom.: 973 Cov.: 32 AF XY: 0.0998 AC XY: 7429 AN XY: 74460

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.0507

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.0191

Gnomad4 SAS AF: 0.0122

Gnomad4 FIN AF: 0.0762

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.0851

Alfa AF: 0.108 Hom.: 1552

Bravo AF: 0.108

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	11
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094061; hg19: chr6-30321189;