chr21-44934070-A-G

Position:

• chr21-44934070-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01547 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01547	NR_027128.1	n.1047T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01547	ENST00000615847.3	n.2056T>C		non_coding_transcript_exon_variant	4/4	1
LINC01547	ENST00000397841.5	n.1047T>C		non_coding_transcript_exon_variant	4/4	2
LINC01547	ENST00000654166.2	n.2224T>C		non_coding_transcript_exon_variant	4/4

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

Gnomad4 AFR exome AF: 0.835

Gnomad4 AMR exome AF: 0.431

Gnomad4 ASJ exome AF: 0.353

Gnomad4 EAS exome AF: 0.282

Gnomad4 SAS exome AF: 0.220

Gnomad4 FIN exome AF: 0.354

Gnomad4 NFE exome AF: 0.344

Gnomad4 OTH exome AF: 0.347

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

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.430

Alfa AF: 0.300 Hom.: 1112

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9974152; hg19: chr21-46353985; COSMIC: COSV57936849;