rs2942168

Positions:

• chr17-45637484-G-A
• chr17-45637484-G-C
• chr17-45637484-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001256299.3(LINC02210-CRHR1):​c.-493+7326G>A variant causes a intron 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-CRHR1 NM_001256299.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

LINC02210-CRHR1 (HGNC:):

LINC02210 (HGNC:26327): (long intergenic non-protein coding RNA 2210)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001256299.3	c.-493+7326G>A		intron_variant			NP_001243228.1
LINC02210	NR_138260.1	n.624+6878G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02210	ENST00000455565.5	n.2134G>A		non_coding_transcript_exon_variant	4/4	1
LINC02210	ENST00000591271.5	n.422+7326G>A		intron_variant, non_coding_transcript_variant		3
LINC02210	ENST00000586362.1	n.201+83G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR exome AF: 0.0667

Gnomad4 AMR exome AF: 0.154

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.0789

Gnomad4 NFE exome AF: 0.193

Gnomad4 OTH exome AF: 0.148

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

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0738

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.183

Alfa AF: 0.199 Hom.: 4625

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	-0.83
CADD	Benign	0.14
DANN	Benign	0.82

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: rs2942168; hg19: chr17-43714850;