rs17074118

chr13-29948080-G-A

Variant summary

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

The NR_033889.1(LINC00544):n.524+309G>A variant causes a intron, non coding transcript 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 NR_033889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00544	NR_033889.1	n.524+309G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00544	ENST00000400540.5	n.859+309G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.0964

Gnomad4 OTH AF: 0.116

Alfa AF: 0.107 Hom.: 1317

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17074118; hg19: chr13-30522217;