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. The variant received -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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.354 AC: 14642 AN: 41420

American (AMR) AF: 0.378 AC: 5771 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 928 AN: 3468

East Asian (EAS) AF: 0.350 AC: 1805 AN: 5160

South Asian (SAS) AF: 0.151 AC: 728 AN: 4824

European-Finnish (FIN) AF: 0.198 AC: 2089 AN: 10540

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12906 AN: 67994

Other (OTH) AF: 0.266 AC: 562 AN: 2110

Alfa AF: 0.191 Hom.: 1778

Bravo AF: 0.285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.18
DANN	Benign	0.50
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs4743420; hg19: chr9-103488089;