rs17119434

Positions:

• chr10-105745403-A-G

Variant summary

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

The NR_120625.1(LINC02627):​n.431-71715T>C 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 0.0872 in 152,200 control chromosomes in the GnomAD database, including 1,525 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 0.087 (1525 hom., cov: 32)
• Consequence: LINC02627 NR_120625.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

LINC02627 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02627	NR_120625.1	n.431-71715T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13246 AN: 152082 Hom.: 1526 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.00772

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0872 AC: 13273 AN: 152200 Hom.: 1525 Cov.: 32 AF XY: 0.0863 AC XY: 6422 AN XY: 74426

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.0350

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.0422

Gnomad4 SAS AF: 0.0845

Gnomad4 FIN AF: 0.00772

Gnomad4 NFE AF: 0.0109

Gnomad4 OTH AF: 0.0780

Alfa AF: 0.0353 Hom.: 195

Bravo AF: 0.0954

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17119434; hg19: chr10-107505161;