chr13-54530436-G-A

Position:

• chr13-54530436-G-A

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 0.842 in 152,032 control chromosomes in the GnomAD database, including 54,038 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 0.84 (54038 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

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 (AFR) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127863 AN: 151916 Hom.: 53982 Cov.: 31

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.842 AC: 127980 AN: 152032 Hom.: 54038 Cov.: 31 AF XY: 0.836 AC XY: 62121 AN XY: 74300

Gnomad4 AFR AF: 0.921

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.837

Alfa AF: 0.834 Hom.: 20352

Bravo AF: 0.843

Asia WGS AF: 0.829 AC: 2877 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1341622; hg19: chr13-55104571;