chr13-46542816-G-A

Position:

• chr13-46542816-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 0.352 in 151,982 control chromosomes in the GnomAD database, including 11,620 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 0.35 (11620 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53494 AN: 151864 Hom.: 11612 Cov.: 32

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.352 AC: 53511 AN: 151982 Hom.: 11620 Cov.: 32 AF XY: 0.359 AC XY: 26677 AN XY: 74284

Gnomad4 AFR AF: 0.0837

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.372

Alfa AF: 0.399 Hom.: 2145

Bravo AF: 0.330

Asia WGS AF: 0.373 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2405414; hg19: chr13-47116951;