13-75043482-G-A

Position:

• chr13-75043482-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 0.478 in 151,254 control chromosomes in the GnomAD database, including 19,054 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 0.48 (19054 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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: 0.478 AC: 72270 AN: 151138 Hom.: 19051 Cov.: 30

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.478 AC: 72281 AN: 151254 Hom.: 19054 Cov.: 30 AF XY: 0.477 AC XY: 35249 AN XY: 73884

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.511

Alfa AF: 0.514 Hom.: 3516

Bravo AF: 0.468

Asia WGS AF: 0.497 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1340900; hg19: chr13-75617619;