rs13123551

Variant names:

• chr4-154527912-T-A
• rs13123551

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 0.525 in 152,018 control chromosomes in the GnomAD database, including 21,203 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 0.52 (21203 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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: 0.525 AC: 79690 AN: 151900 Hom.: 21191 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.525 AC: 79735 AN: 152018 Hom.: 21203 Cov.: 32 AF XY: 0.525 AC XY: 39010 AN XY: 74288

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.531

Alfa AF: 0.529 Hom.: 2045

Bravo AF: 0.519

Asia WGS AF: 0.635 AC: 2203 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.086

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13123551; hg19: chr4-155449064;