9-7634720-C-T

Position:

• chr9-7634720-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 0.187 in 151,694 control chromosomes in the GnomAD database, including 2,843 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 0.19 (2843 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.7634720C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28425 AN: 151576 Hom.: 2842 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.187 AC: 28426 AN: 151694 Hom.: 2843 Cov.: 32 AF XY: 0.191 AC XY: 14175 AN XY: 74138

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.178

Alfa AF: 0.185 Hom.: 1423

Bravo AF: 0.182

Asia WGS AF: 0.212 AC: 735 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1485187; hg19: chr9-7634720; COSMIC: COSV60326546;