rs1438852

Variant names:

• chr2-118838515-C-T
• rs1438852

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 0.522 in 152,064 control chromosomes in the GnomAD database, including 21,538 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 0.52 (21538 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 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: 0.522 AC: 79303 AN: 151946 Hom.: 21522 Cov.: 33

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.522 AC: 79357 AN: 152064 Hom.: 21538 Cov.: 33 AF XY: 0.528 AC XY: 39255 AN XY: 74332

African (AFR) AF: 0.387 AC: 16070 AN: 41474

American (AMR) AF: 0.623 AC: 9526 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1772 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1703 AN: 5172

South Asian (SAS) AF: 0.716 AC: 3440 AN: 4804

European-Finnish (FIN) AF: 0.596 AC: 6309 AN: 10580

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38624 AN: 67964

Other (OTH) AF: 0.514 AC: 1080 AN: 2102

Alfa AF: 0.531 Hom.: 6933

Bravo AF: 0.513

Asia WGS AF: 0.537 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.55
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs1438852; hg19: chr2-119596091;