13-64530191-A-T

Variant names:

• chr13-64530191-A-T
• rs12872078

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 0.0696 in 152,144 control chromosomes in the GnomAD database, including 425 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 0.070 (425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0802 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: 0.0697 AC: 10597 AN: 152026 Hom.: 424 Cov.: 32

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0696 AC: 10594 AN: 152144 Hom.: 425 Cov.: 32 AF XY: 0.0691 AC XY: 5143 AN XY: 74404

Gnomad4 AFR AF: 0.0520

Gnomad4 AMR AF: 0.0592

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0248

Gnomad4 SAS AF: 0.0468

Gnomad4 FIN AF: 0.0744

Gnomad4 NFE AF: 0.0820

Gnomad4 OTH AF: 0.0734

Alfa AF: 0.0364 Hom.: 22

Bravo AF: 0.0685

Asia WGS AF: 0.0330 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12872078; hg19: chr13-65104323;