rs17026471

Variant names:

• chr12-97125651-G-A
• rs17026471
• ENST00000552238.1:n.40-59425G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000552238.1(ENSG00000258131):​n.40-59425G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,060 control chromosomes in the GnomAD database, including 1,610 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 0.12 (1610 hom., cov: 32)
• Consequence: ENSG00000258131 ENST00000552238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

Genes affected

ENSG00000258131 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 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
ENSG00000258131	ENST00000552238.1	n.40-59425G>A		intron_variant	Intron 1 of 1	4
ENSG00000257470	ENST00000668647.1	n.298-1585G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18889 AN: 151942 Hom.: 1598 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.125 AC: 18938 AN: 152060 Hom.: 1610 Cov.: 32 AF XY: 0.126 AC XY: 9396 AN XY: 74346

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.0908

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0757

Gnomad4 NFE AF: 0.0620

Gnomad4 OTH AF: 0.124

Alfa AF: 0.109 Hom.: 186

Bravo AF: 0.139

Asia WGS AF: 0.131 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17026471; hg19: chr12-97519429;