9-74302924-C-T

Position:

• chr9-74302924-C-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 0.443 in 151,784 control chromosomes in the GnomAD database, including 16,424 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 0.44 (16424 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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: 0.443 AC: 67193 AN: 151666 Hom.: 16428 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.443 AC: 67192 AN: 151784 Hom.: 16424 Cov.: 31 AF XY: 0.451 AC XY: 33411 AN XY: 74160

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.443

Alfa AF: 0.481 Hom.: 23523

Bravo AF: 0.431

Asia WGS AF: 0.550 AC: 1912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10746953; hg19: chr9-76917840;