13-105448286-A-G

Variant names:

• chr13-105448286-A-G
• rs1253464

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.794 AC: 32931 AN: 41492

American (AMR) AF: 0.663 AC: 10125 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2253 AN: 3466

East Asian (EAS) AF: 0.901 AC: 4662 AN: 5172

South Asian (SAS) AF: 0.645 AC: 3113 AN: 4826

European-Finnish (FIN) AF: 0.655 AC: 6932 AN: 10576

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42988 AN: 67964

Other (OTH) AF: 0.678 AC: 1431 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.37
DANN	Benign	0.41
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1253464; hg19: chr13-106100635;