rs4743598

Variant names:

• chr9-96156151-A-G
• rs4743598

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 0.162 in 152,232 control chromosomes in the GnomAD database, including 2,195 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 0.16 (2195 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 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: 0.162 AC: 24615 AN: 152114 Hom.: 2196 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.162 AC: 24625 AN: 152232 Hom.: 2195 Cov.: 32 AF XY: 0.165 AC XY: 12267 AN XY: 74430

African (AFR) AF: 0.120 AC: 4986 AN: 41534

American (AMR) AF: 0.129 AC: 1969 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3472

East Asian (EAS) AF: 0.359 AC: 1856 AN: 5176

South Asian (SAS) AF: 0.253 AC: 1219 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1622 AN: 10600

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11243 AN: 68014

Other (OTH) AF: 0.203 AC: 428 AN: 2112

Alfa AF: 0.169 Hom.: 9693

Bravo AF: 0.157

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.023
DANN	Benign	0.43
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4743598; hg19: chr9-98918433;