rs6054906

Variant names:

• chr20-7314256-G-A
• rs6054906

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 0.556 in 151,822 control chromosomes in the GnomAD database, including 24,072 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 0.56 (24072 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 4 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 = 0.685 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84346 AN: 151702 Hom.: 24043 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.556 AC: 84429 AN: 151822 Hom.: 24072 Cov.: 32 AF XY: 0.552 AC XY: 40974 AN XY: 74196

African (AFR) AF: 0.692 AC: 28660 AN: 41426

American (AMR) AF: 0.581 AC: 8850 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2006 AN: 3466

East Asian (EAS) AF: 0.434 AC: 2236 AN: 5150

South Asian (SAS) AF: 0.441 AC: 2123 AN: 4812

European-Finnish (FIN) AF: 0.442 AC: 4649 AN: 10508

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.502 AC: 34059 AN: 67912

Other (OTH) AF: 0.573 AC: 1211 AN: 2114

Alfa AF: 0.583 Hom.: 10272

Bravo AF: 0.571

Asia WGS AF: 0.478 AC: 1659 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.75
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs6054906; hg19: chr20-7294903; COSMIC: COSV56533147;