5-74188595-G-T

Position:

• chr5-74188595-G-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01331	ENST00000663633.1	n.324-75444C>A		intron_variant, non_coding_transcript_variant

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;