chr17-45782039-T-A

Variant names:

• chr17-45782039-T-A
• rs12942300
• ENST00000634540.1:c.-492-24971T>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.-492-24971T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,984 control chromosomes in the GnomAD database, including 1,244 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 0.11 (1244 hom., cov: 32)
• Consequence: LINC02210-CRHR1 ENST00000634540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232
• Publications: 8 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=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001303016.1	c.-184-24971T>A		intron_variant	Intron 3 of 12		NP_001289945.1
LINC02210-CRHR1	NM_001256299.3	c.-492-24971T>A		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.-492-24971T>A		intron_variant	Intron 3 of 14	2		ENSP00000488912.1
LINC02210-CRHR1	ENST00000587305.1	n.448-24971T>A		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17395 AN: 151866 Hom.: 1242 Cov.: 32

Gnomad AFR AF: 0.0557

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.115 AC: 17405 AN: 151984 Hom.: 1244 Cov.: 32 AF XY: 0.109 AC XY: 8087 AN XY: 74266

African (AFR) AF: 0.0558 AC: 2310 AN: 41432

American (AMR) AF: 0.0917 AC: 1402 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 376 AN: 3460

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5164

South Asian (SAS) AF: 0.108 AC: 521 AN: 4818

European-Finnish (FIN) AF: 0.105 AC: 1112 AN: 10556

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11244 AN: 67958

Other (OTH) AF: 0.0970 AC: 204 AN: 2104

Alfa AF: 0.138 Hom.: 220

Bravo AF: 0.109

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	14
DANN	Benign	0.90
PhyloP100		-0.23
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: rs12942300; hg19: chr17-43859405;