9-119744674-C-T

Variant names:

• chr9-119744674-C-T
• rs7030915

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 0.528 in 151,898 control chromosomes in the GnomAD database, including 21,325 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 0.53 (21325 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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: 0.528 AC: 80214 AN: 151780 Hom.: 21329 Cov.: 31

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.528 AC: 80235 AN: 151898 Hom.: 21325 Cov.: 31 AF XY: 0.529 AC XY: 39242 AN XY: 74242

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.527

Alfa AF: 0.539 Hom.: 10083

Bravo AF: 0.529

Asia WGS AF: 0.594 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7030915; hg19: chr9-122506952; COSMIC: COSV60399691;