chr6-30094133-G-A

Position:

• chr6-30094133-G-A

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 0.235 in 152,132 control chromosomes in the GnomAD database, including 5,453 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 0.23 (5453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35658 AN: 152014 Hom.: 5445 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.235 AC: 35691 AN: 152132 Hom.: 5453 Cov.: 32 AF XY: 0.230 AC XY: 17104 AN XY: 74388

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.0507

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.266

Alfa AF: 0.219 Hom.: 735

Bravo AF: 0.261

Asia WGS AF: 0.245 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.58
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17194174; hg19: chr6-30061910;