rs11655470

Positions:

• chr17-45718067-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.-493+87909C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,730 control chromosomes in the GnomAD database, including 10,822 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 0.37 (10822 hom., cov: 29)
• Consequence: LINC02210-CRHR1 NM_001256299.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

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 (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02210-CRHR1	NM_001256299.3	c.-493+87909C>T		intron_variant			NP_001243228.1
LINC02210-CRHR1	NM_001303016.1	c.-185+45165C>T		intron_variant			NP_001289945.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55932 AN: 151610 Hom.: 10812 Cov.: 29

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.369 AC: 55964 AN: 151730 Hom.: 10822 Cov.: 29 AF XY: 0.376 AC XY: 27837 AN XY: 74094

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.366

Alfa AF: 0.397 Hom.: 18450

Bravo AF: 0.353

Asia WGS AF: 0.428 AC: 1487 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	6.6
DANN	Benign	0.70

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: rs11655470; hg19: chr17-43795433;