rs17119490

chr10-105763169-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120625.1(LINC02627):n.430+54749C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 152,100 control chromosomes in the GnomAD database, including 667 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 0.061 (667 hom., cov: 32)
• Consequence: LINC02627 NR_120625.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

Genes affected

LINC02627 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02627	NR_120625.1	n.430+54749C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0612 AC: 9303 AN: 151982 Hom.: 665 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.0414

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.00785

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0106

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0613 AC: 9321 AN: 152100 Hom.: 667 Cov.: 32 AF XY: 0.0614 AC XY: 4565 AN XY: 74366

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0251

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.0415

Gnomad4 SAS AF: 0.0888

Gnomad4 FIN AF: 0.00785

Gnomad4 NFE AF: 0.0106

Gnomad4 OTH AF: 0.0655

Alfa AF: 0.0304 Hom.: 95

Bravo AF: 0.0664

Asia WGS AF: 0.101 AC: 350 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.8
Dann	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17119490; hg19: chr10-107522927;