rs4743420

Variant names:

• chr9-100725807-C-A
• rs4743420

Your query was ambiguous. Multiple possible variants found:

• chr9-100725807-C-A
• chr9-100725807-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 0.261 in 152,000 control chromosomes in the GnomAD database, including 5,744 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 0.26 (5744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 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: 0.261 AC: 39619 AN: 151882 Hom.: 5730 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.261 AC: 39667 AN: 152000 Hom.: 5744 Cov.: 32 AF XY: 0.263 AC XY: 19510 AN XY: 74264

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.266

Alfa AF: 0.189 Hom.: 1583

Bravo AF: 0.285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.18
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4743420; hg19: chr9-103488089;