chr12-102202345-G-A

Variant names:

• chr12-102202345-G-A
• rs7973796
• ENST00000626826.1:n.4761G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000626826.1(HELLPAR):​n.4761G>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 0.559 in 151,990 control chromosomes in the GnomAD database, including 24,950 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 0.56 (24950 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 7 publications found

Genes affected

HELLPAR (HGNC:43984): (HELLP associated long non-coding RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000626826.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HELLPAR	ENST00000626826.1	TSL:6	n.4761G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84845 AN: 151870 Hom.: 24889 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.543

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.559 AC: 84969 AN: 151990 Hom.: 24950 Cov.: 32 AF XY: 0.557 AC XY: 41347 AN XY: 74296

African (AFR) AF: 0.755 AC: 31341 AN: 41488

American (AMR) AF: 0.471 AC: 7189 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1545 AN: 3462

East Asian (EAS) AF: 0.606 AC: 3136 AN: 5178

South Asian (SAS) AF: 0.422 AC: 2035 AN: 4824

European-Finnish (FIN) AF: 0.517 AC: 5435 AN: 10520

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32510 AN: 67938

Other (OTH) AF: 0.546 AC: 1152 AN: 2110

Alfa AF: 0.519 Hom.: 31328

Bravo AF: 0.568

Asia WGS AF: 0.571 AC: 1980 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7973796; hg19: chr12-102596123;