chr10-131775901-G-A

Variant names:

• chr10-131775901-G-A
• rs4897783
• ENST00000341866.3:n.728C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000341866.3(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 ENST00000341866.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.930
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.042).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000341866.3. 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
	LINC01164	NR_038365.1		n.728C>T		non_coding_transcript_exon	Exon 3 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01164	ENST00000341866.3	TSL:2	n.728C>T		non_coding_transcript_exon	Exon 3 of 5
	LINC01164	ENST00000655798.1		n.619C>T		non_coding_transcript_exon	Exon 2 of 6
	LINC01164	ENST00000667493.1		n.619C>T		non_coding_transcript_exon	Exon 2 of 4

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

GnomAD2 exomes AF: 0.517 AC: 70495 AN: 136244 AF XY: 0.505

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 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

African (AFR) AF: 0.576 AC: 4971 AN: 8626

American (AMR) AF: 0.683 AC: 18619 AN: 27274

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 5388 AN: 10790

East Asian (EAS) AF: 0.451 AC: 4152 AN: 9210

South Asian (SAS) AF: 0.453 AC: 27056 AN: 59742

European-Finnish (FIN) AF: 0.465 AC: 5953 AN: 12794

Middle Eastern (MID) AF: 0.455 AC: 1265 AN: 2782

European-Non Finnish (NFE) AF: 0.491 AC: 78044 AN: 158944

Other (OTH) AF: 0.487 AC: 6927 AN: 14236

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

African (AFR) AF: 0.566 AC: 23423 AN: 41410

American (AMR) AF: 0.608 AC: 9285 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1767 AN: 3468

East Asian (EAS) AF: 0.452 AC: 2313 AN: 5120

South Asian (SAS) AF: 0.439 AC: 2097 AN: 4772

European-Finnish (FIN) AF: 0.489 AC: 5167 AN: 10568

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33064 AN: 67876

Other (OTH) AF: 0.481 AC: 1012 AN: 2104

Alfa AF: 0.500 Hom.: 68720

Bravo AF: 0.531

Asia WGS AF: 0.457 AC: 1590 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.4
DANN	Benign	0.95
PhyloP100		0.93
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4897783; hg19: chr10-133608237;