chr11-12058704-C-A

Position:

• chr11-12058704-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531559.1(LINC02547):​n.227C>A 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 0.561 in 152,226 control chromosomes in the GnomAD database, including 24,412 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 0.56 (24403 hom., cov: 34)
  • Exomes 𝑓: 0.62 (9 hom.)
• Consequence: LINC02547 ENST00000531559.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

Genes affected

LINC02547 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02547	NR_135109.1	n.227C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02547	ENST00000531559.1	n.227C>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85291 AN: 152066 Hom.: 24382 Cov.: 34

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.561

GnomAD4 exome AF: 0.619 AC: 26 AN: 42 Hom.: 9 Cov.: 0 AF XY: 0.588 AC XY: 20 AN XY: 34

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.647

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.561 AC: 85355 AN: 152184 Hom.: 24403 Cov.: 34 AF XY: 0.566 AC XY: 42108 AN XY: 74382

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.561

Alfa AF: 0.561 Hom.: 5244

Bravo AF: 0.552

Asia WGS AF: 0.562 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.6
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2403569; hg19: chr11-12080251;