rs1106381

Variant names:

• chr12-102368678-T-G
• rs1106381
• ENST00000626826.1:n.171094T>G

Variant summary

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

The ENST00000626826.1(HELLPAR):​n.171094T>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 0.0354 in 152,336 control chromosomes in the GnomAD database, including 371 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 0.035 (371 hom., cov: 32)
  • Exomes 𝑓: 0.012 (0 hom.)
• Consequence: HELLPAR ENST00000626826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 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.171094T>G		non_coding_transcript_exon	Exon 1 of 1
	LINC02456	ENST00000635615.1	TSL:5	n.449+19746T>G		intron	N/A
	LINC02456	ENST00000704346.1		n.1066+19746T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0353 AC: 5377 AN: 152136 Hom.: 366 Cov.: 32

Gnomad AFR AF: 0.00644

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0991

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.0560

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0430

GnomAD4 exome AF: 0.0122 AC: 1 AN: 82 Hom.: 0 Cov.: 0 AF XY: 0.0161 AC XY: 1 AN XY: 62

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 74

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

GnomAD4 genome AF: 0.0354 AC: 5390 AN: 152254 Hom.: 371 Cov.: 32 AF XY: 0.0406 AC XY: 3024 AN XY: 74434

African (AFR) AF: 0.00642 AC: 267 AN: 41568

American (AMR) AF: 0.0999 AC: 1527 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00374 AC: 13 AN: 3472

East Asian (EAS) AF: 0.282 AC: 1452 AN: 5156

South Asian (SAS) AF: 0.0563 AC: 271 AN: 4816

European-Finnish (FIN) AF: 0.0792 AC: 840 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0137 AC: 929 AN: 68028

Other (OTH) AF: 0.0430 AC: 91 AN: 2114

Alfa AF: 0.0228 Hom.: 19

Bravo AF: 0.0374

Asia WGS AF: 0.188 AC: 650 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.92
DANN	Benign	0.26
PhyloP100		-0.075

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: rs1106381;

hg19: chr12-102762456;