5-97188217-G-T

Position:

• chr5-97188217-G-T

Variant summary

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

The ENST00000506562.1(ENSG00000248758):​n.66C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,926 control chromosomes in the GnomAD database, including 11,354 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 0.38 (11353 hom., cov: 31)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: ENST00000506562.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558

Genes affected

(HGNC:):

LIX1-AS1 (HGNC:52976): (LIX1 and RIOK2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000506562.1	n.66C>A		non_coding_transcript_exon_variant	2/2	3
LIX1-AS1	ENST00000504578.2	n.971+4548G>T		intron_variant, non_coding_transcript_variant		5
	ENST00000654632.1	n.90+4301G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57364 AN: 151802 Hom.: 11344 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.406

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 2 AN XY: 8

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.378 AC: 57388 AN: 151918 Hom.: 11353 Cov.: 31 AF XY: 0.373 AC XY: 27709 AN XY: 74232

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.406

Alfa AF: 0.436 Hom.: 29884

Bravo AF: 0.385

Asia WGS AF: 0.383 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4869151; hg19: chr5-96523921;