rs2054670

chr8-60670274-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 0.569 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;