3-52811089-T-C

Variant names:

• chr3-52811089-T-C
• rs2535627

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 0.532 in 152,048 control chromosomes in the GnomAD database, including 22,186 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 0.53 (22186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 70 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 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: 0.531 AC: 80744 AN: 151930 Hom.: 22168 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.532 AC: 80814 AN: 152048 Hom.: 22186 Cov.: 32 AF XY: 0.528 AC XY: 39239 AN XY: 74280

African (AFR) AF: 0.668 AC: 27712 AN: 41468

American (AMR) AF: 0.583 AC: 8915 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3470

East Asian (EAS) AF: 0.437 AC: 2251 AN: 5156

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4814

European-Finnish (FIN) AF: 0.447 AC: 4726 AN: 10578

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

European-Non Finnish (NFE) AF: 0.472 AC: 32084 AN: 67960

Other (OTH) AF: 0.505 AC: 1067 AN: 2114

Alfa AF: 0.483 Hom.: 24044

Bravo AF: 0.550

Asia WGS AF: 0.449 AC: 1561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.2
DANN	Benign	0.57
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs2535627; hg19: chr3-52845105;