rs73628692

Positions:

• chr9-129587318-A-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 0.0753 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0479

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.00820

Gnomad4 NFE AF: 0.0370

Gnomad4 OTH AF: 0.0859

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73628692; hg19: chr9-132349597;