rs1724422

Positions:

• chr17-45699947-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+69789A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,034 control chromosomes in the GnomAD database, including 16,987 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 0.46 (16987 hom., cov: 32)
• Consequence: LINC02210-CRHR1 NM_001256299.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

Genes affected

LINC02210-CRHR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001256299.3	c.-493+69789A>G		intron_variant			NP_001243228.1
LINC02210-CRHR1	NM_001303016.1	c.-185+27045A>G		intron_variant			NP_001289945.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70265 AN: 151916 Hom.: 16979 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.463 AC: 70320 AN: 152034 Hom.: 16987 Cov.: 32 AF XY: 0.449 AC XY: 33384 AN XY: 74310

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.492

Alfa AF: 0.452 Hom.: 26267

Bravo AF: 0.481

Asia WGS AF: 0.249 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.72
DANN	Benign	0.58

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: rs1724422; hg19: chr17-43777313;