rs1536284

Variant names:

• chr13-75051678-C-T
• rs1536284

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 0.502 in 151,792 control chromosomes in the GnomAD database, including 20,152 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 0.50 (20152 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 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: 0.502 AC: 76202 AN: 151674 Hom.: 20141 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.502 AC: 76231 AN: 151792 Hom.: 20152 Cov.: 31 AF XY: 0.501 AC XY: 37181 AN XY: 74154

African (AFR) AF: 0.327 AC: 13561 AN: 41416

American (AMR) AF: 0.550 AC: 8377 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1994 AN: 3472

East Asian (EAS) AF: 0.521 AC: 2663 AN: 5110

South Asian (SAS) AF: 0.433 AC: 2085 AN: 4818

European-Finnish (FIN) AF: 0.581 AC: 6122 AN: 10532

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39607 AN: 67886

Other (OTH) AF: 0.525 AC: 1108 AN: 2110

Alfa AF: 0.525 Hom.: 3751

Bravo AF: 0.496

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.074
DANN	Benign	0.30
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1536284; hg19: chr13-75625815;