8-19987865-C-T

Variant names:

• chr8-19987865-C-T
• rs7841189

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 0.145 in 152,198 control chromosomes in the GnomAD database, including 1,755 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 (1755 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

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 = 0.212 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: 0.145 AC: 22088 AN: 152080 Hom.: 1755 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.145 AC: 22095 AN: 152198 Hom.: 1755 Cov.: 32 AF XY: 0.142 AC XY: 10582 AN XY: 74410

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0993

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.134

Alfa AF: 0.131 Hom.: 2367

Bravo AF: 0.149

Asia WGS AF: 0.117 AC: 409 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	1.9
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7841189; hg19: chr8-19845376;