ENST00000634540.1:c.-493+87909C>T

Variant names:

• chr17-45718067-C-T
• rs11655470
• ENST00000634540.1:c.-493+87909C>T

Variant summary

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

The ENST00000634540.1(LINC02210-CRHR1):​c.-493+87909C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,730 control chromosomes in the GnomAD database, including 10,822 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 0.37 (10822 hom., cov: 29)
• Consequence: LINC02210-CRHR1 ENST00000634540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 30 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]

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 (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001303016.1	c.-185+45165C>T		intron_variant	Intron 3 of 12		NP_001289945.1
LINC02210-CRHR1	NM_001256299.3	c.-493+87909C>T		intron_variant	Intron 3 of 14		NP_001243228.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02210-CRHR1	ENST00000634540.1	c.-493+87909C>T		intron_variant	Intron 3 of 14	2		ENSP00000488912.1
LINC02210-CRHR1	ENST00000587305.1	n.447+45165C>T		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55932 AN: 151610 Hom.: 10812 Cov.: 29

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.369 AC: 55964 AN: 151730 Hom.: 10822 Cov.: 29 AF XY: 0.376 AC XY: 27837 AN XY: 74094

African (AFR) AF: 0.247 AC: 10218 AN: 41420

American (AMR) AF: 0.356 AC: 5433 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1294 AN: 3458

East Asian (EAS) AF: 0.497 AC: 2552 AN: 5130

South Asian (SAS) AF: 0.482 AC: 2320 AN: 4810

European-Finnish (FIN) AF: 0.501 AC: 5247 AN: 10464

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27649 AN: 67898

Other (OTH) AF: 0.366 AC: 771 AN: 2106

Alfa AF: 0.388 Hom.: 31650

Bravo AF: 0.353

Asia WGS AF: 0.428 AC: 1487 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	6.6
DANN	Benign	0.70
PhyloP100		-0.074
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: rs11655470; hg19: chr17-43795433;