21-44934070-A-G

Variant names:

• chr21-44934070-A-G
• rs9974152
• ENST00000615847.3:n.2056T>C

Variant summary

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

The ENST00000615847.3(LINC01547):​n.2056T>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 0.398 in 362,152 control chromosomes in the GnomAD database, including 34,850 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 (21723 hom., cov: 33)
  • Exomes 𝑓: 0.34 (13127 hom.)
• Consequence: LINC01547 ENST00000615847.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 6 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=-0.92).
• 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.1047T>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.2056T>C		non_coding_transcript_exon_variant	Exon 4 of 4	1
LINC01547	ENST00000397841.5	n.1047T>C		non_coding_transcript_exon_variant	Exon 4 of 4	2
LINC01547	ENST00000654166.2	n.2224T>C		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73704 AN: 151972 Hom.: 21677 Cov.: 33

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.434

GnomAD4 exome AF: 0.335 AC: 70404 AN: 210062 Hom.: 13127 Cov.: 0 AF XY: 0.320 AC XY: 36989 AN XY: 115620

African (AFR) AF: 0.835 AC: 4377 AN: 5244

American (AMR) AF: 0.431 AC: 5040 AN: 11682

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1480 AN: 4190

East Asian (EAS) AF: 0.282 AC: 2347 AN: 8318

South Asian (SAS) AF: 0.220 AC: 9304 AN: 42290

European-Finnish (FIN) AF: 0.354 AC: 7325 AN: 20708

Middle Eastern (MID) AF: 0.328 AC: 223 AN: 680

European-Non Finnish (NFE) AF: 0.344 AC: 37038 AN: 107524

Other (OTH) AF: 0.347 AC: 3270 AN: 9426

GnomAD4 genome AF: 0.485 AC: 73808 AN: 152090 Hom.: 21723 Cov.: 33 AF XY: 0.480 AC XY: 35644 AN XY: 74322

African (AFR) AF: 0.837 AC: 34738 AN: 41516

American (AMR) AF: 0.448 AC: 6841 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1282 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1379 AN: 5154

South Asian (SAS) AF: 0.208 AC: 1002 AN: 4816

European-Finnish (FIN) AF: 0.351 AC: 3717 AN: 10582

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23486 AN: 67954

Other (OTH) AF: 0.430 AC: 910 AN: 2114

Alfa AF: 0.325 Hom.: 1396

Bravo AF: 0.513

Asia WGS AF: 0.283 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.36
PhyloP100		-0.16
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: rs9974152; hg19: chr21-46353985; COSMIC: COSV57936849;