chr6-30904497-G-A

Variant names:

• chr6-30904497-G-A
• rs2894054

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.153 AC: 6327 AN: 41422

American (AMR) AF: 0.0915 AC: 1397 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0909 AC: 315 AN: 3466

East Asian (EAS) AF: 0.0678 AC: 351 AN: 5174

South Asian (SAS) AF: 0.0413 AC: 199 AN: 4814

European-Finnish (FIN) AF: 0.0686 AC: 724 AN: 10558

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0796 AC: 5412 AN: 67978

Other (OTH) AF: 0.0863 AC: 182 AN: 2108

Alfa AF: 0.0866 Hom.: 1594

Bravo AF: 0.105

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.35
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs2894054; hg19: chr6-30872274;