chr13-75051678-C-T

Variant names:

• chr13-75051678-C-T
• rs1536284

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.525

Alfa AF: 0.531 Hom.: 3714

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1536284; hg19: chr13-75625815;