rs28575156

chr6-31442080-A-Gchr6-31442080-A-T

Variant summary

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

The NR_144465.1(LINC01149):n.414A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,724 control chromosomes in the GnomAD database, including 4,267 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 0.22 (4265 hom., cov: 30)
  • Exomes 𝑓: 0.19 (2 hom.)
• Consequence: LINC01149 NR_144465.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

Genes affected

LINC01149 (HGNC:39757): (long intergenic non-protein coding RNA 1149)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01149	NR_144465.1	n.414A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01149	ENST00000430364.1	n.414A>G		non_coding_transcript_exon_variant	1/2	1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32825 AN: 151470 Hom.: 4257 Cov.: 30

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.205

GnomAD4 exome AF: 0.188 AC: 26 AN: 138 Hom.: 2 Cov.: 0 AF XY: 0.167 AC XY: 16 AN XY: 96

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.300

Gnomad4 NFE exome AF: 0.174

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.217 AC: 32870 AN: 151586 Hom.: 4265 Cov.: 30 AF XY: 0.222 AC XY: 16435 AN XY: 74092

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.204

Alfa AF: 0.158 Hom.: 1332

Bravo AF: 0.222

Asia WGS AF: 0.200 AC: 692 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.2
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28575156; hg19: chr6-31409857;