chr9-102829080-T-C

Variant names:

• chr9-102829080-T-C
• rs843258

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 0.551 in 151,934 control chromosomes in the GnomAD database, including 23,921 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 0.55 (23921 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.689 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83638 AN: 151816 Hom.: 23903 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.551 AC: 83696 AN: 151934 Hom.: 23921 Cov.: 32 AF XY: 0.546 AC XY: 40563 AN XY: 74248

African (AFR) AF: 0.695 AC: 28834 AN: 41464

American (AMR) AF: 0.467 AC: 7112 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1601 AN: 3468

East Asian (EAS) AF: 0.514 AC: 2642 AN: 5138

South Asian (SAS) AF: 0.306 AC: 1478 AN: 4828

European-Finnish (FIN) AF: 0.541 AC: 5706 AN: 10554

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34723 AN: 67948

Other (OTH) AF: 0.517 AC: 1089 AN: 2106

Alfa AF: 0.544 Hom.: 2971

Bravo AF: 0.555

Asia WGS AF: 0.389 AC: 1350 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.74
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs843258; hg19: chr9-105591362;