13-105448286-A-G

Position:

• chr13-105448286-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 0.691 in 152,076 control chromosomes in the GnomAD database, including 36,818 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 0.69 (36818 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.691 AC: 105029 AN: 151958 Hom.: 36776 Cov.: 33

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.691 AC: 105131 AN: 152076 Hom.: 36818 Cov.: 33 AF XY: 0.692 AC XY: 51414 AN XY: 74338

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.678

Alfa AF: 0.652 Hom.: 6596

Bravo AF: 0.696

Asia WGS AF: 0.759 AC: 2620 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.37
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1253464; hg19: chr13-106100635;