rs1880753

chr17-45733894-G-A

Variant summary

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

The NM_001256299.3(LINC02210-CRHR1):c.-492-73116G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,048 control chromosomes in the GnomAD database, including 18,279 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 0.47 (18279 hom., cov: 32)
• Consequence: LINC02210-CRHR1 NM_001256299.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.438

Genes affected

LINC02210-CRHR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02210-CRHR1	NM_001256299.3	c.-492-73116G>A		intron_variant
LOC107985028	XR_001752915.2	n.396+390C>T		intron_variant, non_coding_transcript_variant
LINC02210-CRHR1	NM_001303016.1	c.-185+60992G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000580347.1	n.387-368C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71401 AN: 151930 Hom.: 18270 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.451

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.470 AC: 71425 AN: 152048 Hom.: 18279 Cov.: 32 AF XY: 0.479 AC XY: 35580 AN XY: 74324

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.454

Alfa AF: 0.529 Hom.: 39076

Bravo AF: 0.450

Asia WGS AF: 0.479 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.1
Dann	Benign	0.31

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: rs1880753; hg19: chr17-43811260;