rs10860861

Variant names:

• chr12-102391791-C-T
• rs10860861
• ENST00000626826.1:n.194207C>T

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.194207C>T 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 0.554 in 152,078 control chromosomes in the GnomAD database, including 24,035 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 0.55 (24022 hom., cov: 31)
  • Exomes 𝑓: 0.55 (13 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 9 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 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.194207C>T		non_coding_transcript_exon	Exon 1 of 1
	LINC02456	ENST00000635615.1	TSL:5	n.450-31280C>T		intron	N/A
	LINC02456	ENST00000704346.1		n.1067-31280C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84143 AN: 151880 Hom.: 23973 Cov.: 31

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.552

GnomAD4 exome AF: 0.550 AC: 44 AN: 80 Hom.: 13 Cov.: 0 AF XY: 0.483 AC XY: 28 AN XY: 58

African (AFR) AF: 0.500 AC: 1 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) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.565 AC: 35 AN: 62

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.554 AC: 84259 AN: 151998 Hom.: 24022 Cov.: 31 AF XY: 0.553 AC XY: 41063 AN XY: 74288

African (AFR) AF: 0.693 AC: 28729 AN: 41462

American (AMR) AF: 0.480 AC: 7328 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1542 AN: 3470

East Asian (EAS) AF: 0.629 AC: 3239 AN: 5152

South Asian (SAS) AF: 0.407 AC: 1964 AN: 4822

European-Finnish (FIN) AF: 0.560 AC: 5912 AN: 10558

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33787 AN: 67954

Other (OTH) AF: 0.556 AC: 1170 AN: 2106

Alfa AF: 0.507 Hom.: 22855

Bravo AF: 0.559

Asia WGS AF: 0.567 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.8
DANN	Benign	0.36
PhyloP100		0.32

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: rs10860861;

hg19: chr12-102785569;