10-131775901-G-A

Position:

• chr10-131775901-G-A

Variant summary

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

The NR_038365.1(LINC01164):​n.728C>T 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 0.507 in 456,182 control chromosomes in the GnomAD database, including 59,986 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 0.52 (20824 hom., cov: 30)
  • Exomes 𝑓: 0.50 (39162 hom.)
• Consequence: LINC01164 NR_038365.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.930

Genes affected

LINC01164 (HGNC:49533): (long intergenic non-protein coding RNA 1164)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01164	NR_038365.1	n.728C>T		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01164	ENST00000341866.3	n.728C>T		non_coding_transcript_exon_variant	3/5	2

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78772 AN: 151666 Hom.: 20808 Cov.: 30

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.484

GnomAD3 exomes AF: 0.517 AC: 70495 AN: 136244 Hom.: 18888 AF XY: 0.505 AC XY: 37434 AN XY: 74134

Gnomad AFR exome AF: 0.583

Gnomad AMR exome AF: 0.683

Gnomad ASJ exome AF: 0.499

Gnomad EAS exome AF: 0.444

Gnomad SAS exome AF: 0.449

Gnomad FIN exome AF: 0.471

Gnomad NFE exome AF: 0.486

Gnomad OTH exome AF: 0.504

GnomAD4 exome AF: 0.501 AC: 152375 AN: 304398 Hom.: 39162 Cov.: 0 AF XY: 0.491 AC XY: 85116 AN XY: 173332

Gnomad4 AFR exome AF: 0.576

Gnomad4 AMR exome AF: 0.683

Gnomad4 ASJ exome AF: 0.499

Gnomad4 EAS exome AF: 0.451

Gnomad4 SAS exome AF: 0.453

Gnomad4 FIN exome AF: 0.465

Gnomad4 NFE exome AF: 0.491

Gnomad4 OTH exome AF: 0.487

GnomAD4 genome AF: 0.519 AC: 78829 AN: 151784 Hom.: 20824 Cov.: 30 AF XY: 0.520 AC XY: 38604 AN XY: 74184

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.481

Alfa AF: 0.492 Hom.: 41597

Bravo AF: 0.531

Asia WGS AF: 0.457 AC: 1590 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.4
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4897783; hg19: chr10-133608237;