rs7228576

Positions:

• chr18-10408495-C-T

Variant summary

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

The NR_110775.1(LINC01254):​n.1591-2280G>A 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 0.183 in 152,050 control chromosomes in the GnomAD database, including 3,246 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 0.18 (3246 hom., cov: 32)
• Consequence: LINC01254 NR_110775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

LINC01254 (HGNC:49870): (long intergenic non-protein coding RNA 1254)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01254	NR_110775.1	n.1591-2280G>A		intron_variant, non_coding_transcript_variant
LOC105371988	XR_935142.4	n.737+1551C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01254	ENST00000567609.1	n.1591-2280G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000671418.1	n.387+1551C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27745 AN: 151932 Hom.: 3246 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0660

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.183 AC: 27773 AN: 152050 Hom.: 3246 Cov.: 32 AF XY: 0.177 AC XY: 13158 AN XY: 74328

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0660

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.177

Alfa AF: 0.147 Hom.: 2476

Bravo AF: 0.191

Asia WGS AF: 0.107 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7228576; hg19: chr18-10408492;