rs1919811

chr7-53811760-C-Achr7-53811760-C-G

Variant summary

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

The NR_038371.1(LINC01446):n.172G>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 0.548 in 152,806 control chromosomes in the GnomAD database, including 23,494 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 0.55 (23386 hom., cov: 32)
  • Exomes 𝑓: 0.49 (108 hom.)
• Consequence: LINC01446 NR_038371.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

LINC01446 (HGNC:50773): (long intergenic non-protein coding RNA 1446)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01446	NR_038371.1	n.172G>T		non_coding_transcript_exon_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01446	ENST00000380970.2	n.172G>T		non_coding_transcript_exon_variant	1/6	2

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83285 AN: 151892 Hom.: 23356 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.494 AC: 393 AN: 796 Hom.: 108 Cov.: 0 AF XY: 0.528 AC XY: 279 AN XY: 528

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.750

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.700

Gnomad4 FIN exome AF: 0.498

Gnomad4 NFE exome AF: 0.476

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.548 AC: 83368 AN: 152010 Hom.: 23386 Cov.: 32 AF XY: 0.551 AC XY: 40906 AN XY: 74296

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.564

Alfa AF: 0.472 Hom.: 3540

Bravo AF: 0.557

Asia WGS AF: 0.547 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1919811; hg19: chr7-53879453;