9-7634720-C-T

Variant names:

• chr9-7634720-C-T
• rs1485187

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.129 AC: 5361 AN: 41426

American (AMR) AF: 0.205 AC: 3115 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 541 AN: 3466

East Asian (EAS) AF: 0.316 AC: 1618 AN: 5126

South Asian (SAS) AF: 0.170 AC: 819 AN: 4816

European-Finnish (FIN) AF: 0.292 AC: 3073 AN: 10522

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13296 AN: 67824

Other (OTH) AF: 0.178 AC: 374 AN: 2098

Alfa AF: 0.191 Hom.: 2002

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
PhyloP100		1.1

Splicing

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

Other links and lift over

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