rs1724425

Positions:

• chr17-45704381-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001303016.1(LINC02210-CRHR1):​c.-185+31479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,056 control chromosomes in the GnomAD database, including 12,334 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 0.40 (12334 hom., cov: 32)
• Consequence: LINC02210-CRHR1 NM_001303016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343

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]

LINC02210-CRHR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001303016.1	c.-185+31479C>T		intron_variant			NP_001289945.1
LINC02210-CRHR1	NM_001256299.3	c.-493+74223C>T		intron_variant			NP_001243228.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02210-CRHR1	ENST00000634540.1	c.-493+74223C>T		intron_variant		2		ENSP00000488912.1
LINC02210-CRHR1	ENST00000587305.1	n.447+31479C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60524 AN: 151938 Hom.: 12318 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.398 AC: 60579 AN: 152056 Hom.: 12334 Cov.: 32 AF XY: 0.388 AC XY: 28836 AN XY: 74336

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.441

Alfa AF: 0.422 Hom.: 9591

Bravo AF: 0.411

Asia WGS AF: 0.261 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs1724425; hg19: chr17-43781747;