rs12128558

chr1-5509431-C-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 0.0895 in 152,216 control chromosomes in the GnomAD database, including 678 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 0.090 (678 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 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: 0.0895 AC: 13616 AN: 152098 Hom.: 678 Cov.: 33

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0391

Gnomad FIN AF: 0.0841

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0969

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

GnomAD4 genome AF: 0.0895 AC: 13625 AN: 152216 Hom.: 678 Cov.: 33 AF XY: 0.0874 AC XY: 6501 AN XY: 74414

Gnomad4 AFR AF: 0.0876

Gnomad4 AMR AF: 0.0690

Gnomad4 ASJ AF: 0.0663

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0391

Gnomad4 FIN AF: 0.0841

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0959

Alfa AF: 0.0992 Hom.: 406

Bravo AF: 0.0886

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.36
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12128558; hg19: chr1-5569491;