rs7215239

Positions:

• chr17-45690407-T-C

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+60249T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,072 control chromosomes in the GnomAD database, including 8,480 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 0.29 (8480 hom., cov: 32)
• Consequence: LINC02210-CRHR1 NM_001256299.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.61

Genes affected

LINC02210-CRHR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02210-CRHR1	NM_001256299.3	c.-493+60249T>C		intron_variant
LINC02210-CRHR1	NM_001303016.1	c.-185+17505T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44692 AN: 151954 Hom.: 8460 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.00772

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.294 AC: 44756 AN: 152072 Hom.: 8480 Cov.: 32 AF XY: 0.279 AC XY: 20732 AN XY: 74348

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.00793

Gnomad4 SAS AF: 0.0994

Gnomad4 FIN AF: 0.0744

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.299

Alfa AF: 0.247 Hom.: 7968

Bravo AF: 0.318

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0030
DANN	Benign	0.25

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: rs7215239; hg19: chr17-43767773;