rs3095089

chr6-30966017-G-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 0.156 in 152,158 control chromosomes in the GnomAD database, including 2,058 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 0.16 (2058 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.178 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: 0.156 AC: 23781 AN: 152040 Hom.: 2053 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0141

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.156 AC: 23795 AN: 152158 Hom.: 2058 Cov.: 32 AF XY: 0.148 AC XY: 10989 AN XY: 74394

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.141

Alfa AF: 0.168 Hom.: 2370

Bravo AF: 0.159

Asia WGS AF: 0.0220 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.41
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3095089; hg19: chr6-30933794;