rs4245562

Positions:

• chr7-54336292-T-C
• chr7-54336292-T-G

Variant summary

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

The NR_120515.1(LINC01445):​n.122+5474T>C 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 0.276 in 152,024 control chromosomes in the GnomAD database, including 6,500 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 0.28 (6500 hom., cov: 32)
• Consequence: LINC01445 NR_120515.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853

Genes affected

LINC01445 (HGNC:50771): (long intergenic non-protein coding RNA 1445)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01445	NR_120515.1	n.122+5474T>C		intron_variant, non_coding_transcript_variant
LINC01445	NR_120516.1	n.122+5474T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01445	ENST00000659445.1	n.28+5474T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41971 AN: 151906 Hom.: 6493 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.272

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.276 AC: 42005 AN: 152024 Hom.: 6500 Cov.: 32 AF XY: 0.282 AC XY: 20919 AN XY: 74296

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.272

Alfa AF: 0.319 Hom.: 4194

Bravo AF: 0.265

Asia WGS AF: 0.355 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.094
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4245562; hg19: chr7-54403985;