chr2-4838243-G-A

Variant names:

• chr2-4838243-G-A
• rs1595752

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 0.165 in 152,128 control chromosomes in the GnomAD database, including 2,371 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 0.17 (2371 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 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: 0.165 AC: 25136 AN: 152010 Hom.: 2376 Cov.: 33

Gnomad AFR AF: 0.0904

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.165 AC: 25149 AN: 152128 Hom.: 2371 Cov.: 33 AF XY: 0.172 AC XY: 12757 AN XY: 74342

Gnomad4 AFR AF: 0.0907

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.186

Alfa AF: 0.170 Hom.: 1096

Bravo AF: 0.166

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1595752; hg19: chr2-4885833;