17-45727828-T-G

Position:

• chr17-45727828-T-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.-492-79182T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 146,376 control chromosomes in the GnomAD database, including 26,410 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 0.59 (26410 hom., cov: 27)
• Consequence: LINC02210-CRHR1 NM_001256299.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576

Genes affected

LINC02210-CRHR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001256299.3	c.-492-79182T>G		intron_variant			NP_001243228.1
LINC02210-CRHR1	NM_001303016.1	c.-185+54926T>G		intron_variant			NP_001289945.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.594 AC: 86874 AN: 146282 Hom.: 26391 Cov.: 27

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.594 AC: 86926 AN: 146376 Hom.: 26410 Cov.: 27 AF XY: 0.595 AC XY: 42363 AN XY: 71232

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.554

Alfa AF: 0.538 Hom.: 40239

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.62

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: rs9303521; hg19: chr17-43805194;