13-37489219-C-T

Variant names:

• chr13-37489219-C-T
• rs17055889
• ENST00000827669.1:n.322-1208C>T

Variant summary

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

The ENST00000827669.1(ENSG00000307651):​n.322-1208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0791 in 152,070 control chromosomes in the GnomAD database, including 1,148 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 0.079 (1148 hom., cov: 32)
• Consequence: ENSG00000307651 ENST00000827669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 0 publications found

Genes affected

ENSG00000307651 (HGNC:):

LINC01048 (HGNC:49042): (long intergenic non-protein coding RNA 1048)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.22 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827669.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307651	ENST00000827669.1		n.322-1208C>T		intron	N/A
	LINC01048	ENST00000827904.1		n.103-4826G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0789 AC: 11991 AN: 151952 Hom.: 1143 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.00594

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0160

Gnomad OTH AF: 0.0728

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0791 AC: 12022 AN: 152070 Hom.: 1148 Cov.: 32 AF XY: 0.0801 AC XY: 5956 AN XY: 74332

African (AFR) AF: 0.224 AC: 9290 AN: 41486

American (AMR) AF: 0.0409 AC: 624 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3470

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5178

South Asian (SAS) AF: 0.115 AC: 556 AN: 4824

European-Finnish (FIN) AF: 0.00594 AC: 63 AN: 10604

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0160 AC: 1089 AN: 67940

Other (OTH) AF: 0.0716 AC: 151 AN: 2110

Alfa AF: 0.0233 Hom.: 39

Bravo AF: 0.0858

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.65
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs17055889; hg19: chr13-38063356;