chr8-139507274-G-T

Variant names:

• chr8-139507274-G-T
• rs2468677

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 0.539 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.540

Alfa AF: 0.532 Hom.: 9873

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2468677; hg19: chr8-140519517;