rs4743556

Variant names:

• chr9-96122663-C-T
• rs4743556

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 0.228 in 152,034 control chromosomes in the GnomAD database, including 4,428 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 0.23 (4428 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.353 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: 0.228 AC: 34601 AN: 151914 Hom.: 4404 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.228 AC: 34674 AN: 152034 Hom.: 4428 Cov.: 33 AF XY: 0.235 AC XY: 17461 AN XY: 74328

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.240

Alfa AF: 0.183 Hom.: 6006

Bravo AF: 0.244

Asia WGS AF: 0.355 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4743556; hg19: chr9-98884945;