chr21-44933397-A-G

Variant names:

• chr21-44933397-A-G
• rs7283236
• ENST00000615847.3:n.2729T>C

Variant summary

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

The ENST00000615847.3(LINC01547):​n.2729T>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 ENST00000615847.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 12 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=-0.94).
• 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 rank	MANE	Protein	UniProt
LINC01547	NR_027128.1	n.1720T>C		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01547	ENST00000615847.3	n.2729T>C		non_coding_transcript_exon_variant	Exon 4 of 4	1
LINC01547	ENST00000397841.5	n.1720T>C		non_coding_transcript_exon_variant	Exon 4 of 4	2
LINC01547	ENST00000654166.2	n.2897T>C		non_coding_transcript_exon_variant	Exon 4 of 4

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.375 AC: 6 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.261 AC: 12 AN: 46

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.837 AC: 34719 AN: 41490

American (AMR) AF: 0.451 AC: 6888 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1391 AN: 3466

East Asian (EAS) AF: 0.267 AC: 1380 AN: 5160

South Asian (SAS) AF: 0.210 AC: 1015 AN: 4824

European-Finnish (FIN) AF: 0.352 AC: 3723 AN: 10582

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.350 AC: 23811 AN: 67940

Other (OTH) AF: 0.435 AC: 920 AN: 2116

Alfa AF: 0.388 Hom.: 15471

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
PhyloP100		-1.2
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: rs7283236; hg19: chr21-46353312;