12-102370439-T-G

Position:

• chr12-102370439-T-G

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.172855T>G 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 0.545 in 152,028 control chromosomes in the GnomAD database, including 22,988 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 0.54 (22987 hom., cov: 33)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

Genes affected

HELLPAR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.696+21507T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HELLPAR	ENST00000626826.1	n.172855T>G		non_coding_transcript_exon_variant	1/1	6
LINC02456	ENST00000635615.1	n.449+21507T>G		intron_variant		5
LINC02456	ENST00000704346.1	n.1066+21507T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82730 AN: 151904 Hom.: 22959 Cov.: 33

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.543

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.545 AC: 82809 AN: 152022 Hom.: 22987 Cov.: 33 AF XY: 0.543 AC XY: 40380 AN XY: 74310

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.547

Alfa AF: 0.291 Hom.: 538

Bravo AF: 0.547

Asia WGS AF: 0.574 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2139570; hg19: chr12-102764217;