5-74188595-G-T

Variant names:

• chr5-74188595-G-T
• rs16871467
• ENST00000663633.1:n.324-75444C>A

Variant summary

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

The ENST00000663633.1(LINC01331):​n.324-75444C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0341 in 152,190 control chromosomes in the GnomAD database, including 192 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 0.034 (192 hom., cov: 32)
• Consequence: LINC01331 ENST00000663633.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01331	ENST00000663633.1	n.324-75444C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0340 AC: 5172 AN: 152072 Hom.: 192 Cov.: 32

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0341 AC: 5183 AN: 152190 Hom.: 192 Cov.: 32 AF XY: 0.0340 AC XY: 2533 AN XY: 74418

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.0178

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.0180

Gnomad4 SAS AF: 0.0892

Gnomad4 FIN AF: 0.00283

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0188 Hom.: 17

Bravo AF: 0.0361

Asia WGS AF: 0.0660 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.47
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16871467; hg19: chr5-73484420;