chr21-33170482-A-G

Variant names:

• chr21-33170482-A-G
• rs6517147
• ENST00000451980.5:n.109+82T>C

Variant summary

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

The ENST00000451980.5(LINC01548):​n.109+82T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 309,544 control chromosomes in the GnomAD database, including 7,308 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 0.22 (4078 hom., cov: 31)
  • Exomes 𝑓: 0.19 (3230 hom.)
• Consequence: LINC01548 ENST00000451980.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 4 publications found

Genes affected

LINC01548 (HGNC:1296): (long intergenic non-protein coding RNA 1548)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451980.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01548	NR_024102.1		n.-246T>C		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01548	ENST00000451980.5	TSL:5	n.109+82T>C		intron	N/A
	LINC01548	ENST00000796078.1		n.92+82T>C		intron	N/A
	LINC01548	ENST00000796079.1		n.88+82T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33495 AN: 151784 Hom.: 4076 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.191 AC: 30180 AN: 157642 Hom.: 3230 AF XY: 0.189 AC XY: 16066 AN XY: 85204

African (AFR) AF: 0.286 AC: 1387 AN: 4844

American (AMR) AF: 0.149 AC: 1567 AN: 10518

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 954 AN: 3610

East Asian (EAS) AF: 0.00178 AC: 14 AN: 7856

South Asian (SAS) AF: 0.166 AC: 4898 AN: 29482

European-Finnish (FIN) AF: 0.152 AC: 949 AN: 6238

Middle Eastern (MID) AF: 0.205 AC: 111 AN: 542

European-Non Finnish (NFE) AF: 0.216 AC: 18747 AN: 86732

Other (OTH) AF: 0.199 AC: 1553 AN: 7820

GnomAD4 genome AF: 0.221 AC: 33520 AN: 151902 Hom.: 4078 Cov.: 31 AF XY: 0.215 AC XY: 15968 AN XY: 74240

African (AFR) AF: 0.289 AC: 11959 AN: 41382

American (AMR) AF: 0.184 AC: 2810 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5182

South Asian (SAS) AF: 0.157 AC: 753 AN: 4810

European-Finnish (FIN) AF: 0.137 AC: 1443 AN: 10564

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.220 AC: 14949 AN: 67928

Other (OTH) AF: 0.219 AC: 460 AN: 2104

Alfa AF: 0.221 Hom.: 7326

Bravo AF: 0.226

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6517147; hg19: chr21-34542787;