13-29941416-A-G

Variant names:

• chr13-29941416-A-G
• rs646983
• ENST00000400540.5:n.690+3407A>G

Variant summary

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

The ENST00000400540.5(LINC00544):​n.690+3407A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,116 control chromosomes in the GnomAD database, including 44,020 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 0.76 (44020 hom., cov: 32)
• Consequence: LINC00544 ENST00000400540.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400540.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00544	NR_033889.1		n.355+3407A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00544	ENST00000400540.5	TSL:5	n.690+3407A>G		intron	N/A
	LINC00544	ENST00000481738.2	TSL:3	n.293-478A>G		intron	N/A
	LINC00544	ENST00000656266.1		n.619-681A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115195 AN: 151998 Hom.: 43987 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.758 AC: 115285 AN: 152116 Hom.: 44020 Cov.: 32 AF XY: 0.756 AC XY: 56256 AN XY: 74366

African (AFR) AF: 0.826 AC: 34230 AN: 41456

American (AMR) AF: 0.739 AC: 11297 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2502 AN: 3472

East Asian (EAS) AF: 0.984 AC: 5105 AN: 5188

South Asian (SAS) AF: 0.762 AC: 3669 AN: 4814

European-Finnish (FIN) AF: 0.691 AC: 7308 AN: 10580

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.715 AC: 48638 AN: 68000

Other (OTH) AF: 0.755 AC: 1596 AN: 2114

Alfa AF: 0.736 Hom.: 151369

Bravo AF: 0.767

Asia WGS AF: 0.861 AC: 2992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.74
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs646983; hg19: chr13-30515553;