ENST00000578000.5:n.545A>G

Variant names:

• chr17-45639519-A-G
• rs413778
• ENST00000578000.5:n.545A>G

Variant summary

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

The ENST00000578000.5(LINC02210):​n.545A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,210 control chromosomes in the GnomAD database, including 2,145 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.14 (2145 hom., cov: 31)
  • Exomes 𝑓: 0.18 (0 hom.)
• Consequence: LINC02210 ENST00000578000.5 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 33 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02210	NR_138257.1	n.2155A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 5 of 6
LINC02210	NR_138259.1	n.1964A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 5 of 7
LINC02210-CRHR1	NM_001303016.1	c.-261+9361A>G		intron_variant	Intron 2 of 12		NP_001289945.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02210-CRHR1	ENST00000634540.1	c.-493+9361A>G		intron_variant	Intron 3 of 14	2		ENSP00000488912.1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21840 AN: 152064 Hom.: 2147 Cov.: 31

Gnomad AFR AF: 0.0429

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.179 AC: 5 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.278 AC XY: 5 AN XY: 18

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.182 AC: 4 AN: 22

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.143 AC: 21830 AN: 152182 Hom.: 2145 Cov.: 31 AF XY: 0.134 AC XY: 9998 AN XY: 74408

African (AFR) AF: 0.0428 AC: 1778 AN: 41538

American (AMR) AF: 0.176 AC: 2694 AN: 15266

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

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5182

South Asian (SAS) AF: 0.0737 AC: 355 AN: 4814

European-Finnish (FIN) AF: 0.0653 AC: 693 AN: 10612

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14732 AN: 67982

Other (OTH) AF: 0.182 AC: 385 AN: 2110

Alfa AF: 0.196 Hom.: 2030

Bravo AF: 0.149

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.8
DANN	Benign	0.66
PhyloP100		-0.028
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs413778; hg19: chr17-43716885;