13-24673148-A-G

Position:

• chr13-24673148-A-G

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 0.0474 in 152,278 control chromosomes in the GnomAD database, including 221 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 0.047 (221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 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: 0.0473 AC: 7194 AN: 152160 Hom.: 215 Cov.: 32

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0332

Gnomad EAS AF: 0.0673

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0474 AC: 7218 AN: 152278 Hom.: 221 Cov.: 32 AF XY: 0.0470 AC XY: 3496 AN XY: 74460

Gnomad4 AFR AF: 0.0180

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.0332

Gnomad4 EAS AF: 0.0671

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0261

Gnomad4 NFE AF: 0.0593

Gnomad4 OTH AF: 0.0510

Alfa AF: 0.0537 Hom.: 240

Bravo AF: 0.0471

Asia WGS AF: 0.145 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1530530; hg19: chr13-25247286;