chr17-45637484-G-A

Variant names:

• chr17-45637484-G-A
• rs2942168
• ENST00000455565.5:n.2134G>A

Variant summary

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

The ENST00000455565.5(LINC02210):​n.2134G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 153,412 control chromosomes in the GnomAD database, including 2,174 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 0.14 (2159 hom., cov: 32)
  • Exomes 𝑓: 0.14 (15 hom.)
• Consequence: LINC02210 ENST00000455565.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 87 publications found

Genes affected

LINC02210 (HGNC:):

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 (HGNC:26327): (long intergenic non-protein coding RNA 2210)

ARF2P (HGNC:44341):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455565.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02210	NR_026680.3		n.1635G>A		non_coding_transcript_exon	Exon 4 of 4
	LINC02210	NR_027295.2		n.2129G>A		non_coding_transcript_exon	Exon 4 of 4
	LINC02210	NR_138259.1		n.1635G>A		non_coding_transcript_exon	Exon 4 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02210	ENST00000455565.5	TSL:1	n.2134G>A		non_coding_transcript_exon	Exon 4 of 4
	LINC02210-CRHR1	ENST00000634540.1	TSL:2	c.-493+7326G>A		intron	N/A	ENSP00000488912.1
	LINC02210	ENST00000586362.1	TSL:4	n.201+83G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21958 AN: 152076 Hom.: 2161 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.144 AC: 176 AN: 1218 Hom.: 15 Cov.: 0 AF XY: 0.173 AC XY: 108 AN XY: 624

African (AFR) AF: 0.0667 AC: 2 AN: 30

American (AMR) AF: 0.154 AC: 4 AN: 26

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 4 AN: 24

East Asian (EAS) AF: 0.00 AC: 0 AN: 178

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.0789 AC: 12 AN: 152

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.193 AC: 145 AN: 752

Other (OTH) AF: 0.148 AC: 8 AN: 54

GnomAD4 genome AF: 0.144 AC: 21948 AN: 152194 Hom.: 2159 Cov.: 32 AF XY: 0.135 AC XY: 10051 AN XY: 74408

African (AFR) AF: 0.0448 AC: 1860 AN: 41544

American (AMR) AF: 0.178 AC: 2712 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5184

South Asian (SAS) AF: 0.0738 AC: 356 AN: 4822

European-Finnish (FIN) AF: 0.0651 AC: 690 AN: 10604

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.217 AC: 14750 AN: 68002

Other (OTH) AF: 0.183 AC: 387 AN: 2110

Alfa AF: 0.189 Hom.: 7478

Bravo AF: 0.149

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.14
DANN	Benign	0.82
PhyloP100		-1.2
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: rs2942168; hg19: chr17-43714850;