ENST00000634540.1:c.-492-73116G>A

Variant names:

• chr17-45733894-G-A
• rs1880753
• ENST00000634540.1:c.-492-73116G>A

Variant summary

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

The ENST00000634540.1(LINC02210-CRHR1):​c.-492-73116G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,048 control chromosomes in the GnomAD database, including 18,279 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 0.47 (18279 hom., cov: 32)
• Consequence: LINC02210-CRHR1 ENST00000634540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.438
• Publications: 23 publications found

Genes affected

LINC02210-CRHR1 (HGNC:51483): (LINC02210-CRHR1 readthrough) This locus represents naturally occurring readthrough transcription between neighboring genes CRHR1-IT1, CRHR1 intronic transcript 1 (Gene ID: 147081) and CRHR1, corticotropin releasing hormone receptor 1 (Gene ID: 1394) on chromosome 17. The readthrough transcript encodes a protein that shares sequence identity with the product of the CRHR1 gene. [provided by RefSeq, Dec 2016]

ENSG00000265547 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001303016.1	c.-185+60992G>A		intron_variant	Intron 3 of 12		NP_001289945.1
LINC02210-CRHR1	NM_001256299.3	c.-492-73116G>A		intron_variant	Intron 3 of 14		NP_001243228.1
LOC107985028	XR_001752915.2	n.396+390C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02210-CRHR1	ENST00000634540.1	c.-492-73116G>A		intron_variant	Intron 3 of 14	2		ENSP00000488912.1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71401 AN: 151930 Hom.: 18270 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.451

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.470 AC: 71425 AN: 152048 Hom.: 18279 Cov.: 32 AF XY: 0.479 AC XY: 35580 AN XY: 74324

African (AFR) AF: 0.263 AC: 10896 AN: 41474

American (AMR) AF: 0.532 AC: 8136 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1704 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2567 AN: 5164

South Asian (SAS) AF: 0.448 AC: 2155 AN: 4814

European-Finnish (FIN) AF: 0.697 AC: 7378 AN: 10582

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36884 AN: 67938

Other (OTH) AF: 0.454 AC: 960 AN: 2114

Alfa AF: 0.511 Hom.: 63813

Bravo AF: 0.450

Asia WGS AF: 0.479 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.31
PhyloP100		0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1880753; hg19: chr17-43811260;