rs1880756

chr17-45749300-C-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.-492-57710C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,180 control chromosomes in the GnomAD database, including 7,112 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 (7112 hom., cov: 33)
• Consequence: LINC02210-CRHR1 NM_001256299.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407

Genes affected

LINC02210-CRHR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02210-CRHR1	NM_001256299.3	c.-492-57710C>T		intron_variant
LINC02210-CRHR1	NM_001303016.1	c.-184-57710C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43277 AN: 152062 Hom.: 7105 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.285 AC: 43297 AN: 152180 Hom.: 7112 Cov.: 33 AF XY: 0.292 AC XY: 21733 AN XY: 74404

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.270

Alfa AF: 0.325 Hom.: 4587

Bravo AF: 0.267

Asia WGS AF: 0.287 AC: 997 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	4.0
Dann	Benign	0.69

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: rs1880756; hg19: chr17-43826666;