rs4142603

Positions:

• chr9-77154478-T-C

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 0.199 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0723

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.216

Alfa AF: 0.225 Hom.: 829

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4142603; hg19: chr9-79769394;