21-44933397-A-G

Position:

• chr21-44933397-A-G

Variant summary

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

The NR_027128.1(LINC01547):​n.1720T>C 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 0.489 in 152,134 control chromosomes in the GnomAD database, including 21,890 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 0.49 (21885 hom., cov: 32)
  • Exomes 𝑓: 0.30 (5 hom.)
• Consequence: LINC01547 NR_027128.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

LINC01547 (HGNC:15707): (long intergenic non-protein coding RNA 1547) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01547	NR_027128.1	n.1720T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01547	ENST00000615847.3	n.2729T>C		non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74201 AN: 151946 Hom.: 21843 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.300 AC: 21 AN: 70 Hom.: 5 Cov.: 0 AF XY: 0.364 AC XY: 16 AN XY: 44

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.261

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.489 AC: 74301 AN: 152064 Hom.: 21885 Cov.: 32 AF XY: 0.483 AC XY: 35898 AN XY: 74354

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.435

Alfa AF: 0.361 Hom.: 9555

Bravo AF: 0.517

Asia WGS AF: 0.284 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7283236; hg19: chr21-46353312;