rs12953076

chr17-45776649-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.-492-30361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,064 control chromosomes in the GnomAD database, including 1,841 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 0.15 (1841 hom., cov: 32)
• Consequence: LINC02210-CRHR1 NM_001256299.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

LINC02210-CRHR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02210-CRHR1	NM_001256299.3	c.-492-30361C>T		intron_variant
LINC02210-CRHR1	NM_001303016.1	c.-184-30361C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23113 AN: 151946 Hom.: 1839 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0903

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.152 AC: 23140 AN: 152064 Hom.: 1841 Cov.: 32 AF XY: 0.153 AC XY: 11375 AN XY: 74324

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.0813

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.155

Alfa AF: 0.153 Hom.: 2957

Bravo AF: 0.153

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.8
Dann	Benign	0.71

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: rs12953076; hg19: chr17-43854015;