rs2128382

chr8-129807793-C-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 0.15 in 152,160 control chromosomes in the GnomAD database, including 1,749 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 0.15 (1749 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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: 0.150 AC: 22753 AN: 152042 Hom.: 1748 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.150 AC: 22766 AN: 152160 Hom.: 1749 Cov.: 33 AF XY: 0.149 AC XY: 11059 AN XY: 74396

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.178

Alfa AF: 0.158 Hom.: 242

Bravo AF: 0.149

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.8
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2128382; hg19: chr8-130820039;