rs6517147

Positions:

• chr21-33170482-A-G

Variant summary

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

The ENST00000451980.4(LINC01548):​n.86+82T>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 0.206 in 309,544 control chromosomes in the GnomAD database, including 7,308 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 (4078 hom., cov: 31)
  • Exomes 𝑓: 0.19 (3230 hom.)
• Consequence: LINC01548 ENST00000451980.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

Genes affected

LINC01548 (HGNC:1296): (long intergenic non-protein coding RNA 1548)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01548	ENST00000451980.4	n.86+82T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33495 AN: 151784 Hom.: 4076 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.191 AC: 30180 AN: 157642 Hom.: 3230 AF XY: 0.189 AC XY: 16066 AN XY: 85204

Gnomad4 AFR exome AF: 0.286

Gnomad4 AMR exome AF: 0.149

Gnomad4 ASJ exome AF: 0.264

Gnomad4 EAS exome AF: 0.00178

Gnomad4 SAS exome AF: 0.166

Gnomad4 FIN exome AF: 0.152

Gnomad4 NFE exome AF: 0.216

Gnomad4 OTH exome AF: 0.199

GnomAD4 genome AF: 0.221 AC: 33520 AN: 151902 Hom.: 4078 Cov.: 31 AF XY: 0.215 AC XY: 15968 AN XY: 74240

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.219

Alfa AF: 0.218 Hom.: 4069

Bravo AF: 0.226

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6517147; hg19: chr21-34542787;