rs17026471

chr12-97125651-G-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, non coding transcript 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: ENST00000552238.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000552238.1	n.40-59425G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000668647.1	n.298-1585G>A		intron_variant, non_coding_transcript_variant

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;