13-105448286-A-G

Variant names:

• chr13-105448286-A-G
• rs1253464

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;