5-74382559-T-A

Variant names:

• chr5-74382559-T-A
• rs586853
• ENST00000507781.2:n.423-13038A>T

Variant summary

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

The ENST00000507781.2(LINC01331):​n.423-13038A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,220 control chromosomes in the GnomAD database, including 50,235 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 0.81 (50235 hom., cov: 33)
• Consequence: LINC01331 ENST00000507781.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597
• Publications: 8 publications found

Genes affected

LINC01331 (HGNC:50538): (long intergenic non-protein coding RNA 1331)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507781.2. 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
	LINC01331	NR_126354.2		n.220-13038A>T		intron	N/A
	LINC01331	NR_197435.1		n.105-13038A>T		intron	N/A
	LINC01331	NR_197436.1		n.257-13038A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01331	ENST00000507781.2	TSL:4	n.423-13038A>T		intron	N/A
	LINC01331	ENST00000663633.1		n.156-13038A>T		intron	N/A
	LINC01331	ENST00000715757.1		n.220-13038A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123312 AN: 152102 Hom.: 50219 Cov.: 33

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.811 AC: 123380 AN: 152220 Hom.: 50235 Cov.: 33 AF XY: 0.808 AC XY: 60146 AN XY: 74420

African (AFR) AF: 0.797 AC: 33076 AN: 41522

American (AMR) AF: 0.766 AC: 11703 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2950 AN: 3470

East Asian (EAS) AF: 0.573 AC: 2973 AN: 5184

South Asian (SAS) AF: 0.807 AC: 3889 AN: 4820

European-Finnish (FIN) AF: 0.843 AC: 8931 AN: 10600

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 57030 AN: 68016

Other (OTH) AF: 0.807 AC: 1707 AN: 2116

Alfa AF: 0.823 Hom.: 6413

Bravo AF: 0.803

Asia WGS AF: 0.708 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	14
DANN	Benign	0.83
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs586853; hg19: chr5-73678384;