chr21-44938942-T-C

Variant names:

• chr21-44938942-T-C
• rs4143368
• ENST00000615847.3:n.996A>G

Variant summary

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

The ENST00000615847.3(LINC01547):​n.996A>G 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 0.183 in 152,098 control chromosomes in the GnomAD database, including 2,711 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 0.18 (2711 hom., cov: 32)
• Consequence: LINC01547 ENST00000615847.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01547	NR_027128.1	n.321+651A>G		intron_variant	Intron 1 of 3
LINC01547	NR_027129.1	n.321+651A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01547	ENST00000615847.3	n.996A>G		non_coding_transcript_exon_variant	Exon 1 of 4	1
LINC01547	ENST00000330551.3	n.253+651A>G		intron_variant	Intron 1 of 3	1
LINC01547	ENST00000654166.2	n.1000A>G		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27820 AN: 151980 Hom.: 2711 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.155

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.183 AC: 27850 AN: 152098 Hom.: 2711 Cov.: 32 AF XY: 0.183 AC XY: 13578 AN XY: 74354

African (AFR) AF: 0.240 AC: 9969 AN: 41462

American (AMR) AF: 0.230 AC: 3510 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3472

East Asian (EAS) AF: 0.111 AC: 573 AN: 5184

South Asian (SAS) AF: 0.0563 AC: 271 AN: 4814

European-Finnish (FIN) AF: 0.152 AC: 1613 AN: 10588

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10681 AN: 67980

Other (OTH) AF: 0.155 AC: 327 AN: 2114

Alfa AF: 0.180 Hom.: 417

Bravo AF: 0.194

Asia WGS AF: 0.100 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.66
PhyloP100		0.17
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: rs4143368; hg19: chr21-46358857;