ENST00000615847.3:n.2092G>C

Variant names:

• chr21-44934034-C-G
• rs12483718
• ENST00000615847.3:n.2092G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000615847.3(LINC01547):​n.2092G>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 0.167 in 313,972 control chromosomes in the GnomAD database, including 4,681 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 0.16 (2132 hom., cov: 33)
  • Exomes 𝑓: 0.17 (2549 hom.)
• Consequence: LINC01547 ENST00000615847.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615847.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01547	NR_027128.1		n.1083G>C		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01547	ENST00000615847.3	TSL:1	n.2092G>C		non_coding_transcript_exon	Exon 4 of 4
	LINC01547	ENST00000397841.5	TSL:2	n.1083G>C		non_coding_transcript_exon	Exon 4 of 4
	LINC01547	ENST00000654166.2		n.2260G>C		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24849 AN: 152032 Hom.: 2132 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.167

GnomAD4 exome AF: 0.170 AC: 27585 AN: 161822 Hom.: 2549 Cov.: 0 AF XY: 0.170 AC XY: 15099 AN XY: 89062

African (AFR) AF: 0.109 AC: 517 AN: 4764

American (AMR) AF: 0.175 AC: 1862 AN: 10612

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 452 AN: 3172

East Asian (EAS) AF: 0.169 AC: 1284 AN: 7582

South Asian (SAS) AF: 0.155 AC: 5085 AN: 32820

European-Finnish (FIN) AF: 0.192 AC: 2239 AN: 11636

Middle Eastern (MID) AF: 0.204 AC: 98 AN: 480

European-Non Finnish (NFE) AF: 0.178 AC: 14795 AN: 83330

Other (OTH) AF: 0.169 AC: 1253 AN: 7426

GnomAD4 genome AF: 0.163 AC: 24867 AN: 152150 Hom.: 2132 Cov.: 33 AF XY: 0.165 AC XY: 12275 AN XY: 74378

African (AFR) AF: 0.118 AC: 4892 AN: 41510

American (AMR) AF: 0.161 AC: 2464 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3470

East Asian (EAS) AF: 0.159 AC: 822 AN: 5162

South Asian (SAS) AF: 0.150 AC: 723 AN: 4814

European-Finnish (FIN) AF: 0.198 AC: 2099 AN: 10598

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12726 AN: 67992

Other (OTH) AF: 0.165 AC: 349 AN: 2112

Alfa AF: 0.0890 Hom.: 120

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.79
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12483718; hg19: chr21-46353949; COSMIC: COSV57936840;