ENST00000564841.1:n.2065T>C

Variant names:

• chr13-99995845-A-G
• rs1347190
• ENST00000564841.1:n.2065T>C

Variant summary

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

The ENST00000564841.1(LINC00554):​n.2065T>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 0.357 in 152,150 control chromosomes in the GnomAD database, including 10,372 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 0.36 (10372 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LINC00554 ENST00000564841.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 5 publications found

Genes affected

LINC00554 (HGNC:43697): (long intergenic non-protein coding RNA 554)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564841.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00554	NR_047483.1		n.2065T>C		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00554	ENST00000564841.1	TSL:6	n.2065T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54270 AN: 152026 Hom.: 10371 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.396

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.357 AC: 54293 AN: 152146 Hom.: 10372 Cov.: 33 AF XY: 0.351 AC XY: 26141 AN XY: 74372

African (AFR) AF: 0.242 AC: 10061 AN: 41522

American (AMR) AF: 0.343 AC: 5244 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3466

East Asian (EAS) AF: 0.222 AC: 1146 AN: 5172

South Asian (SAS) AF: 0.195 AC: 941 AN: 4826

European-Finnish (FIN) AF: 0.394 AC: 4161 AN: 10550

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29861 AN: 68000

Other (OTH) AF: 0.400 AC: 844 AN: 2112

Alfa AF: 0.411 Hom.: 38823

Bravo AF: 0.354

Asia WGS AF: 0.234 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.84
PhyloP100		0.76

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1347190;

hg19: chr13-100648099;