8-139507274-G-T

Variant names:

• chr8-139507274-G-T
• rs2468677

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 0.539 in 151,962 control chromosomes in the GnomAD database, including 22,255 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 0.54 (22255 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.539 AC: 81886 AN: 151844 Hom.: 22236 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.539 AC: 81943 AN: 151962 Hom.: 22255 Cov.: 32 AF XY: 0.548 AC XY: 40696 AN XY: 74294

African (AFR) AF: 0.513 AC: 21258 AN: 41426

American (AMR) AF: 0.552 AC: 8422 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3470

East Asian (EAS) AF: 0.754 AC: 3888 AN: 5156

South Asian (SAS) AF: 0.545 AC: 2625 AN: 4816

European-Finnish (FIN) AF: 0.603 AC: 6374 AN: 10564

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.525 AC: 35696 AN: 67948

Other (OTH) AF: 0.540 AC: 1140 AN: 2110

Alfa AF: 0.530 Hom.: 49251

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.33
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2468677; hg19: chr8-140519517;