13-105407907-A-G

Position:

• chr13-105407907-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 0.629 in 152,024 control chromosomes in the GnomAD database, including 31,348 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 0.63 (31348 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.629 AC: 95492 AN: 151906 Hom.: 31291 Cov.: 33

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.629 AC: 95611 AN: 152024 Hom.: 31348 Cov.: 33 AF XY: 0.631 AC XY: 46890 AN XY: 74280

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.597

Alfa AF: 0.550 Hom.: 12988

Bravo AF: 0.642

Asia WGS AF: 0.642 AC: 2228 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7329966; hg19: chr13-106060256;