rs2456526

Variant names:

• chr15-52797245-T-C
• rs2456526

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 0.218 in 152,048 control chromosomes in the GnomAD database, including 4,727 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 0.22 (4727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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: 0.218 AC: 33095 AN: 151930 Hom.: 4719 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.218 AC: 33140 AN: 152048 Hom.: 4727 Cov.: 32 AF XY: 0.214 AC XY: 15927 AN XY: 74334

African (AFR) AF: 0.416 AC: 17228 AN: 41418

American (AMR) AF: 0.157 AC: 2397 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3468

East Asian (EAS) AF: 0.214 AC: 1111 AN: 5180

South Asian (SAS) AF: 0.144 AC: 693 AN: 4816

European-Finnish (FIN) AF: 0.104 AC: 1095 AN: 10576

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9700 AN: 67990

Other (OTH) AF: 0.187 AC: 395 AN: 2108

Alfa AF: 0.169 Hom.: 8319

Bravo AF: 0.230

Asia WGS AF: 0.221 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.67
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2456526; hg19: chr15-53089442;