9-129587318-A-T

Variant names:

• chr9-129587318-A-T
• rs73628692

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 0.0753 in 151,858 control chromosomes in the GnomAD database, including 627 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 0.075 (627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 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: 0.0751 AC: 11399 AN: 151740 Hom.: 623 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0479

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.00820

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0369

Gnomad OTH AF: 0.0801

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

GnomAD4 genome AF: 0.0753 AC: 11431 AN: 151858 Hom.: 627 Cov.: 32 AF XY: 0.0762 AC XY: 5655 AN XY: 74244

African (AFR) AF: 0.138 AC: 5709 AN: 41384

American (AMR) AF: 0.101 AC: 1548 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0479 AC: 166 AN: 3468

East Asian (EAS) AF: 0.108 AC: 550 AN: 5116

South Asian (SAS) AF: 0.130 AC: 627 AN: 4808

European-Finnish (FIN) AF: 0.00820 AC: 87 AN: 10608

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0370 AC: 2510 AN: 67906

Other (OTH) AF: 0.0859 AC: 181 AN: 2106

Alfa AF: 0.0549 Hom.: 59

Bravo AF: 0.0828

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs73628692; hg19: chr9-132349597;