rs393152

Positions:

• chr17-45641777-A-G

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+11619A>G variant causes a intron 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-CRHR1 NM_001256299.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

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=-0.91).
• 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/exons	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001256299.3	c.-493+11619A>G		intron_variant			NP_001243228.1
LINC02210	NR_138260.1	n.625-4124A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02210	ENST00000591271.5	n.423-4124A>G		intron_variant, non_coding_transcript_variant		3

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

GnomAD3 exomes AF: 0.179 AC: 24485 AN: 136796 Hom.: 3076 AF XY: 0.173 AC XY: 12851 AN XY: 74236

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 SAS exome AF: 0.0805

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

Gnomad4 AFR exome AF: 0.520

Gnomad4 AMR exome AF: 0.149

Gnomad4 ASJ exome AF: 0.256

Gnomad4 EAS exome AF: 0.000640

Gnomad4 SAS exome AF: 0.0839

Gnomad4 FIN exome AF: 0.0769

Gnomad4 NFE exome AF: 0.213

Gnomad4 OTH exome AF: 0.196

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

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0760

Gnomad4 FIN AF: 0.0655

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.282

Alfa AF: 0.221 Hom.: 7307

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

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: rs393152; hg19: chr17-43719143;