rs1595752

Variant names:

• chr2-4838243-G-A
• rs1595752

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0907 AC: 3767 AN: 41536

American (AMR) AF: 0.225 AC: 3446 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 831 AN: 3470

East Asian (EAS) AF: 0.348 AC: 1788 AN: 5136

South Asian (SAS) AF: 0.297 AC: 1433 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2142 AN: 10562

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11215 AN: 68002

Other (OTH) AF: 0.186 AC: 392 AN: 2110

Alfa AF: 0.169 Hom.: 1205

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
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1595752; hg19: chr2-4885833;