chr9-129729271-C-T

Variant names:

• chr9-129729271-C-T
• rs10988484

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 0.297 in 151,976 control chromosomes in the GnomAD database, including 9,550 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 0.30 (9550 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 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: 0.297 AC: 45092 AN: 151858 Hom.: 9534 Cov.: 31

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.297 AC: 45159 AN: 151976 Hom.: 9550 Cov.: 31 AF XY: 0.295 AC XY: 21938 AN XY: 74272

African (AFR) AF: 0.592 AC: 24527 AN: 41450

American (AMR) AF: 0.218 AC: 3327 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 661 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2131 AN: 5166

South Asian (SAS) AF: 0.322 AC: 1551 AN: 4816

European-Finnish (FIN) AF: 0.129 AC: 1359 AN: 10544

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10658 AN: 67960

Other (OTH) AF: 0.265 AC: 559 AN: 2108

Alfa AF: 0.219 Hom.: 1948

Bravo AF: 0.316

Asia WGS AF: 0.357 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.047
DANN	Benign	0.48
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10988484; hg19: chr9-132491550;