rs4853750

Variant names:

• chr2-190874558-G-A
• rs4853750

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 0.107 in 150,890 control chromosomes in the GnomAD database, including 1,240 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 0.11 (1240 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.256 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: 0.107 AC: 16063 AN: 150806 Hom.: 1231 Cov.: 29

Gnomad AFR AF: 0.0900

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.107 AC: 16081 AN: 150890 Hom.: 1240 Cov.: 29 AF XY: 0.109 AC XY: 8047 AN XY: 73608

Gnomad4 AFR AF: 0.0899

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.0368

Gnomad4 NFE AF: 0.0782

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0906 Hom.: 113

Bravo AF: 0.123

Asia WGS AF: 0.160 AC: 558 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4853750; hg19: chr2-191739284;