chr13-103550825-G-A

Position:

• chr13-103550825-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 0.0858 in 152,020 control chromosomes in the GnomAD database, including 895 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 0.086 (895 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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: 0.0859 AC: 13045 AN: 151902 Hom.: 895 Cov.: 33

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0326

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0704

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

GnomAD4 genome AF: 0.0858 AC: 13045 AN: 152020 Hom.: 895 Cov.: 33 AF XY: 0.0899 AC XY: 6679 AN XY: 74266

Gnomad4 AFR AF: 0.0214

Gnomad4 AMR AF: 0.0518

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0332

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0692

Alfa AF: 0.0966 Hom.: 393

Bravo AF: 0.0687

Asia WGS AF: 0.0800 AC: 276 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9300826; hg19: chr13-104203175;