rs17074118

Variant names:

• chr13-29948080-G-A
• rs17074118
• ENST00000400540.5:n.859+309G>A

Variant summary

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

The ENST00000400540.5(LINC00544):​n.859+309G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,138 control chromosomes in the GnomAD database, including 1,177 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 0.12 (1177 hom., cov: 32)
• Consequence: LINC00544 ENST00000400540.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 2 publications found

Genes affected

LINC00544 (HGNC:43679): (long intergenic non-protein coding RNA 544)

ENSG00000301304 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00544	NR_033889.1	n.524+309G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00544	ENST00000400540.5	n.859+309G>A		intron_variant	Intron 5 of 5	5
LINC00544	ENST00000777689.1	n.321+309G>A		intron_variant	Intron 2 of 2
LINC00544	ENST00000777690.1	n.332+309G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17978 AN: 152020 Hom.: 1173 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0964

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.118 AC: 18003 AN: 152138 Hom.: 1177 Cov.: 32 AF XY: 0.123 AC XY: 9164 AN XY: 74358

African (AFR) AF: 0.119 AC: 4921 AN: 41520

American (AMR) AF: 0.168 AC: 2569 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 541 AN: 3470

East Asian (EAS) AF: 0.180 AC: 927 AN: 5160

South Asian (SAS) AF: 0.146 AC: 701 AN: 4816

European-Finnish (FIN) AF: 0.121 AC: 1283 AN: 10590

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0964 AC: 6555 AN: 67992

Other (OTH) AF: 0.116 AC: 245 AN: 2110

Alfa AF: 0.107 Hom.: 1644

Bravo AF: 0.121

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.5
DANN	Benign	0.66
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs17074118; hg19: chr13-30522217;