rs4490198

Variant names:

• chr2-114406882-G-A
• rs4490198

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 0.539 in 151,996 control chromosomes in the GnomAD database, including 22,688 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 0.54 (22688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 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: 0.539 AC: 81838 AN: 151880 Hom.: 22687 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.539 AC: 81852 AN: 151996 Hom.: 22688 Cov.: 32 AF XY: 0.539 AC XY: 40064 AN XY: 74306

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.592

Alfa AF: 0.567 Hom.: 11624

Bravo AF: 0.547

Asia WGS AF: 0.594 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4490198; hg19: chr2-115164459;