rs4142603

Variant names:

• chr9-77154478-T-C
• rs4142603

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 0.199 in 151,810 control chromosomes in the GnomAD database, including 3,719 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 0.20 (3719 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 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: 0.200 AC: 30270 AN: 151692 Hom.: 3716 Cov.: 31

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.199 AC: 30279 AN: 151810 Hom.: 3719 Cov.: 31 AF XY: 0.206 AC XY: 15289 AN XY: 74186

African (AFR) AF: 0.0723 AC: 3000 AN: 41468

American (AMR) AF: 0.339 AC: 5172 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3468

East Asian (EAS) AF: 0.381 AC: 1971 AN: 5172

South Asian (SAS) AF: 0.272 AC: 1306 AN: 4810

European-Finnish (FIN) AF: 0.257 AC: 2707 AN: 10514

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14588 AN: 67836

Other (OTH) AF: 0.216 AC: 455 AN: 2104

Alfa AF: 0.220 Hom.: 831

Bravo AF: 0.202

Asia WGS AF: 0.312 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.59
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs4142603; hg19: chr9-79769394;