rs2054670

Variant names:

• chr8-60670274-G-T
• rs2054670

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 0.569 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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

African (AFR) AF: 0.718 AC: 29760 AN: 41446

American (AMR) AF: 0.507 AC: 7753 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1920 AN: 3472

East Asian (EAS) AF: 0.617 AC: 3200 AN: 5184

South Asian (SAS) AF: 0.596 AC: 2874 AN: 4820

European-Finnish (FIN) AF: 0.486 AC: 5138 AN: 10576

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34127 AN: 67952

Other (OTH) AF: 0.559 AC: 1179 AN: 2110

Alfa AF: 0.544 Hom.: 10890

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
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs2054670; hg19: chr8-61582833;