rs4252042

Variant names:

• chr2-113134947-G-A
• rs4252042

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 0.0758 in 152,218 control chromosomes in the GnomAD database, including 635 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 0.076 (635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 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: 0.0759 AC: 11537 AN: 152100 Hom.: 634 Cov.: 32

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0430

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0670

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

GnomAD4 genome AF: 0.0758 AC: 11537 AN: 152218 Hom.: 635 Cov.: 32 AF XY: 0.0757 AC XY: 5637 AN XY: 74430

Gnomad4 AFR AF: 0.0203

Gnomad4 AMR AF: 0.0429

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0271

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.100 Hom.: 129

Bravo AF: 0.0635

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4252042; hg19: chr2-113892524;