rs439945

Positions:

• chr17-45649293-A-C
• chr17-45649293-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+19135A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,146 control chromosomes in the GnomAD database, including 35,921 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 0.66 (35914 hom., cov: 32)
  • Exomes 𝑓: 0.67 (7 hom.)
• Consequence: LINC02210-CRHR1 NM_001256299.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001256299.3	c.-493+19135A>C		intron_variant			NP_001243228.1
LINC02210-CRHR1	NM_001303016.1	c.-261+19135A>C		intron_variant			NP_001289945.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02210	ENST00000591271.5	n.3815A>C		non_coding_transcript_exon_variant	4/4	3

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100362 AN: 151996 Hom.: 35897 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.664

GnomAD4 exome AF: 0.667 AC: 20 AN: 30 Hom.: 7 Cov.: 0 AF XY: 0.600 AC XY: 12 AN XY: 20

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.636

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.660 AC: 100415 AN: 152116 Hom.: 35914 Cov.: 32 AF XY: 0.676 AC XY: 50256 AN XY: 74370

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.905

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.669

Alfa AF: 0.726 Hom.: 12120

Bravo AF: 0.631

Asia WGS AF: 0.854 AC: 2969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.43

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: rs439945; hg19: chr17-43726659;