chr12-102241743-C-A

Position:

• chr12-102241743-C-A

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.44159C>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 0.182 in 151,692 control chromosomes in the GnomAD database, including 2,928 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 0.18 (2928 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926

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 (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102241743C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HELLPAR	ENST00000626826.1	n.44159C>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27538 AN: 151566 Hom.: 2901 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.0900

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.196

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.182 AC: 27618 AN: 151684 Hom.: 2928 Cov.: 32 AF XY: 0.183 AC XY: 13539 AN XY: 74150

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.0901

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.200

Alfa AF: 0.163 Hom.: 391

Bravo AF: 0.199

Asia WGS AF: 0.234 AC: 812 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	0.19
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12426318; hg19: chr12-102635521;