rs13155012

Variant names:

• chr5-151166504-G-A
• rs13155012

Your query was ambiguous. Multiple possible variants found:

• chr5-151166504-G-A
• chr5-151166504-G-C

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 0.0573 in 150,148 control chromosomes in the GnomAD database, including 260 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 0.057 (260 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0641 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: 0.0573 AC: 8604 AN: 150034 Hom.: 260 Cov.: 31

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.0123

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.0370

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.0495

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.0506

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

GnomAD4 genome AF: 0.0573 AC: 8608 AN: 150148 Hom.: 260 Cov.: 31 AF XY: 0.0569 AC XY: 4172 AN XY: 73282

Gnomad4 AFR AF: 0.0534

Gnomad4 AMR AF: 0.0655

Gnomad4 ASJ AF: 0.0370

Gnomad4 EAS AF: 0.00368

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.0495

Gnomad4 NFE AF: 0.0657

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0593 Hom.: 51

Bravo AF: 0.0565

Asia WGS AF: 0.0190 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13155012; hg19: chr5-150546065;