chr17-45771129-G-T

Position:

• chr17-45771129-G-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.-184-35881G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,838 control chromosomes in the GnomAD database, including 27,512 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 0.59 (27512 hom., cov: 30)
• Consequence: LINC02210-CRHR1 NM_001303016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001303016.1	c.-184-35881G>T		intron_variant			NP_001289945.1
LINC02210-CRHR1	NM_001256299.3	c.-492-35881G>T		intron_variant			NP_001243228.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02210-CRHR1	ENST00000634540.1	c.-492-35881G>T		intron_variant		2		ENSP00000488912.1
LINC02210-CRHR1	ENST00000587305.1	n.448-35881G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88874 AN: 151720 Hom.: 27515 Cov.: 30

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.585 AC: 88886 AN: 151838 Hom.: 27512 Cov.: 30 AF XY: 0.592 AC XY: 43905 AN XY: 74148

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.606

Alfa AF: 0.624 Hom.: 21666

Bravo AF: 0.574

Asia WGS AF: 0.761 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.039
DANN	Benign	0.72

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: rs7225082; hg19: chr17-43848495;