chr9-117673863-T-C

Variant names:

• chr9-117673863-T-C
• rs4837494

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 0.807 in 151,542 control chromosomes in the GnomAD database, including 49,672 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 0.81 (49672 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.85 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: 0.807 AC: 122242 AN: 151424 Hom.: 49629 Cov.: 28

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.807 AC: 122344 AN: 151542 Hom.: 49672 Cov.: 28 AF XY: 0.804 AC XY: 59501 AN XY: 74004

African (AFR) AF: 0.742 AC: 30658 AN: 41304

American (AMR) AF: 0.859 AC: 13022 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2881 AN: 3466

East Asian (EAS) AF: 0.752 AC: 3817 AN: 5076

South Asian (SAS) AF: 0.872 AC: 4187 AN: 4802

European-Finnish (FIN) AF: 0.716 AC: 7524 AN: 10508

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57485 AN: 67922

Other (OTH) AF: 0.821 AC: 1728 AN: 2104

Alfa AF: 0.839 Hom.: 27389

Bravo AF: 0.813

Asia WGS AF: 0.825 AC: 2871 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	1.6
DANN	Benign	0.59
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs4837494; hg19: chr9-120436141;