6-30353412-A-C

Variant names:

• chr6-30353412-A-C
• rs3094061

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;