chr19-31592813-C-T

Variant names:

• chr19-31592813-C-T
• rs547088716
• ENST00000562167.2:n.1138G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000562167.2(ENSG00000261400):​n.1138G>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 0.0000155 in 1,288,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000026 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000014 (0 hom.)
• Consequence: ENSG00000261400 ENST00000562167.2 non_coding_transcript_exon
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.326
• Publications: 0 publications found

Genes affected

ENSG00000261400 (HGNC:):

LINC03103 (HGNC:48330): (long intergenic non-protein coding RNA 3103)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562167.2. 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
	LINC03103	NR_172934.1		n.646C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC03103	NR_172935.1		n.781C>T		non_coding_transcript_exon	Exon 4 of 4
	LINC03103	NR_172936.1		n.639C>T		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261400	ENST00000562167.2	TSL:1	n.1138G>A		non_coding_transcript_exon	Exon 2 of 2
	LINC03103	ENST00000590611.3	TSL:1	n.748C>T		non_coding_transcript_exon	Exon 4 of 4
	LINC03103	ENST00000592644.1	TSL:1	n.221C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0000263 AC: 4 AN: 152088 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000141 AC: 16 AN: 1136800 Hom.: 0 Cov.: 33 AF XY: 0.0000161 AC XY: 9 AN XY: 557652

African (AFR) AF: 0.00 AC: 0 AN: 24406

American (AMR) AF: 0.00 AC: 0 AN: 28256

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15936

East Asian (EAS) AF: 0.00 AC: 0 AN: 12836

South Asian (SAS) AF: 0.0000131 AC: 1 AN: 76192

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12638

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4396

European-Non Finnish (NFE) AF: 0.0000163 AC: 15 AN: 920632

Other (OTH) AF: 0.00 AC: 0 AN: 41508

GnomAD4 genome AF: 0.0000263 AC: 4 AN: 152088 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74304

African (AFR) AF: 0.0000241 AC: 1 AN: 41424

American (AMR) AF: 0.00 AC: 0 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10608

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 68006

Other (OTH) AF: 0.00 AC: 0 AN: 2086

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000264

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	Inborn genetic diseases (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.96
DANN	Benign	0.71
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs547088716; hg19: chr19-32083719;