2-52681489-T-C

Variant names:

• chr2-52681489-T-C
• rs350792

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 0.641 in 151,928 control chromosomes in the GnomAD database, including 31,802 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 0.64 (31802 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 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: 0.641 AC: 97316 AN: 151810 Hom.: 31755 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.641 AC: 97424 AN: 151928 Hom.: 31802 Cov.: 31 AF XY: 0.645 AC XY: 47880 AN XY: 74258

African (AFR) AF: 0.750 AC: 31086 AN: 41444

American (AMR) AF: 0.690 AC: 10527 AN: 15266

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

East Asian (EAS) AF: 0.683 AC: 3507 AN: 5138

South Asian (SAS) AF: 0.679 AC: 3271 AN: 4816

European-Finnish (FIN) AF: 0.678 AC: 7155 AN: 10558

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38157 AN: 67918

Other (OTH) AF: 0.612 AC: 1292 AN: 2112

Alfa AF: 0.580 Hom.: 44845

Bravo AF: 0.648

Asia WGS AF: 0.721 AC: 2501 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	3.3
DANN	Benign	0.31
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs350792; hg19: chr2-52908627;