rs2894054

chr6-30904497-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 0.0987 in 151,990 control chromosomes in the GnomAD database, including 875 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 0.099 (875 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

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 = 0.15 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: 0.0987 AC: 14983 AN: 151872 Hom.: 873 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.0916

Gnomad ASJ AF: 0.0909

Gnomad EAS AF: 0.0677

Gnomad SAS AF: 0.0415

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0796

Gnomad OTH AF: 0.0877

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

GnomAD4 genome AF: 0.0987 AC: 15009 AN: 151990 Hom.: 875 Cov.: 32 AF XY: 0.0982 AC XY: 7298 AN XY: 74292

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0915

Gnomad4 ASJ AF: 0.0909

Gnomad4 EAS AF: 0.0678

Gnomad4 SAS AF: 0.0413

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.0796

Gnomad4 OTH AF: 0.0863

Alfa AF: 0.0815 Hom.: 740

Bravo AF: 0.105

Asia WGS AF: 0.0680 AC: 235 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	1.8
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2894054; hg19: chr6-30872274;