12-102363335-A-G

Variant names:

• chr12-102363335-A-G
• rs4764695
• ENST00000626826.1:n.165751A>G

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.165751A>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 0.573 in 152,040 control chromosomes in the GnomAD database, including 25,873 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 0.57 (25865 hom., cov: 32)
  • Exomes 𝑓: 0.58 (8 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466
• Publications: 13 publications found

Genes affected

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

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HELLPAR	ENST00000626826.1	TSL:6	n.165751A>G		non_coding_transcript_exon	Exon 1 of 1
	LINC02456	ENST00000635615.1	TSL:5	n.449+14403A>G		intron	N/A
	LINC02456	ENST00000704346.1		n.1066+14403A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86918 AN: 151874 Hom.: 25811 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.564

GnomAD4 exome AF: 0.583 AC: 28 AN: 48 Hom.: 8 Cov.: 0 AF XY: 0.595 AC XY: 25 AN XY: 42

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.611 AC: 22 AN: 36

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.573 AC: 87037 AN: 151992 Hom.: 25865 Cov.: 32 AF XY: 0.572 AC XY: 42505 AN XY: 74302

African (AFR) AF: 0.745 AC: 30893 AN: 41470

American (AMR) AF: 0.486 AC: 7432 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1582 AN: 3462

East Asian (EAS) AF: 0.615 AC: 3168 AN: 5150

South Asian (SAS) AF: 0.437 AC: 2101 AN: 4808

European-Finnish (FIN) AF: 0.557 AC: 5896 AN: 10578

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34151 AN: 67928

Other (OTH) AF: 0.567 AC: 1197 AN: 2112

Alfa AF: 0.525 Hom.: 59472

Bravo AF: 0.578

Asia WGS AF: 0.584 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.41
PhyloP100		0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4764695;

hg19: chr12-102757113;