rs4437724

Variant names:

• chr9-113346815-T-C
• rs4437724

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 0.166 in 151,704 control chromosomes in the GnomAD database, including 2,913 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 0.17 (2913 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 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: 0.166 AC: 25111 AN: 151586 Hom.: 2904 Cov.: 31

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0346

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.166 AC: 25139 AN: 151704 Hom.: 2913 Cov.: 31 AF XY: 0.163 AC XY: 12087 AN XY: 74148

African (AFR) AF: 0.328 AC: 13507 AN: 41216

American (AMR) AF: 0.101 AC: 1544 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3470

East Asian (EAS) AF: 0.0341 AC: 176 AN: 5158

South Asian (SAS) AF: 0.187 AC: 898 AN: 4808

European-Finnish (FIN) AF: 0.0569 AC: 601 AN: 10558

Middle Eastern (MID) AF: 0.117 AC: 34 AN: 290

European-Non Finnish (NFE) AF: 0.109 AC: 7395 AN: 67940

Other (OTH) AF: 0.143 AC: 302 AN: 2108

Alfa AF: 0.131 Hom.: 845

Bravo AF: 0.172

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.92
DANN	Benign	0.67
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4437724; hg19: chr9-116109095;