rs1421292

chr13-105545886-T-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 0.391 in 152,004 control chromosomes in the GnomAD database, including 12,987 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 0.39 (12987 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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: 0.391 AC: 59436 AN: 151886 Hom.: 12979 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.391 AC: 59449 AN: 152004 Hom.: 12987 Cov.: 32 AF XY: 0.393 AC XY: 29229 AN XY: 74306

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.386

Alfa AF: 0.433 Hom.: 1909

Bravo AF: 0.383

Asia WGS AF: 0.401 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.47
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1421292; hg19: chr13-106198235;