rs12438594

Positions:

• chr15-74374851-G-A
• chr15-74374851-G-C

Variant summary

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

The ENST00000611178.1(ENSG00000274937):​n.174G>A 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 0.254 in 152,474 control chromosomes in the GnomAD database, including 6,058 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 0.25 (6046 hom., cov: 32)
  • Exomes 𝑓: 0.17 (12 hom.)
• Consequence: ENSG00000274937 ENST00000611178.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

Genes affected

ENSG00000274937 (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 (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.74374851G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000274937	ENST00000611178.1	n.174G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38596 AN: 151776 Hom.: 6021 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.227

GnomAD4 exome AF: 0.172 AC: 100 AN: 580 Hom.: 12 Cov.: 0 AF XY: 0.193 AC XY: 80 AN XY: 414

Gnomad4 AFR exome AF: 0.571

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.429

Gnomad4 SAS exome AF: 0.625

Gnomad4 FIN exome AF: 0.188

Gnomad4 NFE exome AF: 0.127

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.255 AC: 38687 AN: 151894 Hom.: 6046 Cov.: 32 AF XY: 0.257 AC XY: 19049 AN XY: 74208

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.233

Alfa AF: 0.206 Hom.: 719

Bravo AF: 0.264

Asia WGS AF: 0.434 AC: 1511 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	4.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12438594; hg19: chr15-74667192;