ENST00000578000.5:n.1935A>G

Variant names:

• chr17-45641777-A-G
• rs393152
• ENST00000578000.5:n.1935A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000578000.5(LINC02210):​n.1935A>G 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 0.213 in 457,296 control chromosomes in the GnomAD database, including 14,391 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 0.28 (8008 hom., cov: 32)
  • Exomes 𝑓: 0.18 (6383 hom.)
• Consequence: LINC02210 ENST00000578000.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 123 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)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.042).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02210	NR_138257.1	n.3545A>G		non_coding_transcript_exon_variant	Exon 6 of 6
LINC02210-CRHR1	NM_001303016.1	c.-261+11619A>G		intron_variant	Intron 2 of 12		NP_001289945.1
LINC02210-CRHR1	NM_001256299.3	c.-493+11619A>G		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+11619A>G		intron_variant	Intron 3 of 14	2		ENSP00000488912.1

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42721 AN: 152014 Hom.: 7985 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0766

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.286

GnomAD2 exomes AF: 0.179 AC: 24485 AN: 136796 AF XY: 0.173

Gnomad AFR exome AF: 0.536

Gnomad AMR exome AF: 0.149

Gnomad ASJ exome AF: 0.256

Gnomad EAS exome AF: 0.000666

Gnomad FIN exome AF: 0.0721

Gnomad NFE exome AF: 0.222

Gnomad OTH exome AF: 0.205

GnomAD4 exome AF: 0.179 AC: 54691 AN: 305164 Hom.: 6383 Cov.: 0 AF XY: 0.171 AC XY: 29604 AN XY: 173598

African (AFR) AF: 0.520 AC: 4493 AN: 8640

American (AMR) AF: 0.149 AC: 4071 AN: 27266

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 2773 AN: 10818

East Asian (EAS) AF: 0.000640 AC: 6 AN: 9370

South Asian (SAS) AF: 0.0839 AC: 5008 AN: 59708

European-Finnish (FIN) AF: 0.0769 AC: 997 AN: 12968

Middle Eastern (MID) AF: 0.227 AC: 632 AN: 2786

European-Non Finnish (NFE) AF: 0.213 AC: 33916 AN: 159332

Other (OTH) AF: 0.196 AC: 2795 AN: 14276

GnomAD4 genome AF: 0.281 AC: 42783 AN: 152132 Hom.: 8008 Cov.: 32 AF XY: 0.266 AC XY: 19813 AN XY: 74424

African (AFR) AF: 0.521 AC: 21613 AN: 41466

American (AMR) AF: 0.227 AC: 3462 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 838 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5180

South Asian (SAS) AF: 0.0760 AC: 367 AN: 4826

European-Finnish (FIN) AF: 0.0655 AC: 695 AN: 10614

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14849 AN: 67974

Other (OTH) AF: 0.282 AC: 596 AN: 2112

Alfa AF: 0.231 Hom.: 19198

Bravo AF: 0.305

Asia WGS AF: 0.0640 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.52
PhyloP100		0.065
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: rs393152; hg19: chr17-43719143;