rs1421292

Variant names:

• chr13-105545886-T-A
• rs1421292

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;