rs7841189

Positions:

• chr8-19987865-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 0.145 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;