9-29592838-G-T

Variant names:

• chr9-29592838-G-T
• rs560764

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 0.457 in 151,842 control chromosomes in the GnomAD database, including 16,394 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 0.46 (16394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 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: 0.457 AC: 69324 AN: 151724 Hom.: 16393 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.457 AC: 69344 AN: 151842 Hom.: 16394 Cov.: 32 AF XY: 0.458 AC XY: 33951 AN XY: 74194

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.467

Alfa AF: 0.505 Hom.: 39466

Bravo AF: 0.455

Asia WGS AF: 0.363 AC: 1262 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs560764; hg19: chr9-29592836; COSMIC: COSV60348908;