rs13123551

Positions:

• chr4-154527912-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 0.525 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;