rs2054670

Variant names:

• chr8-60670274-G-T
• rs2054670

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 0.569 in 152,050 control chromosomes in the GnomAD database, including 25,426 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 0.57 (25426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86455 AN: 151932 Hom.: 25391 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.569 AC: 86550 AN: 152050 Hom.: 25426 Cov.: 32 AF XY: 0.569 AC XY: 42258 AN XY: 74314

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.559

Alfa AF: 0.537 Hom.: 6855

Bravo AF: 0.578

Asia WGS AF: 0.624 AC: 2170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2054670; hg19: chr8-61582833;