rs525381

chr12-275626-G-Achr12-275626-G-T

Variant summary

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

The ENST00000570140.1(ENSG00000261799):n.1498C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,978 control chromosomes in the GnomAD database, including 8,497 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 0.31 (8497 hom., cov: 32)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: ENST00000570140.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 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
	ENST00000570140.1	n.1498C>T		non_coding_transcript_exon_variant	1/1
	ENST00000703815.1	n.623G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47695 AN: 151850 Hom.: 8479 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.272

GnomAD4 exome AF: 0.200 AC: 2 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.314 AC: 47750 AN: 151968 Hom.: 8497 Cov.: 32 AF XY: 0.313 AC XY: 23283 AN XY: 74274

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.269

Alfa AF: 0.252 Hom.: 5155

Bravo AF: 0.314

Asia WGS AF: 0.272 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.48
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs525381; hg19: chr12-384792;