rs4245562

Variant names:

• chr7-54336292-T-C
• rs4245562
• ENST00000426205.3:n.119+5474T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426205.3(LINC01445):​n.119+5474T>C variant causes a intron 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 ENST00000426205.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01445	NR_120515.1	n.122+5474T>C		intron_variant	Intron 1 of 2
LINC01445	NR_120516.1	n.122+5474T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01445	ENST00000426205.3	n.119+5474T>C		intron_variant	Intron 1 of 2	3
LINC01445	ENST00000458615.5	n.122+5474T>C		intron_variant	Intron 1 of 2	2
LINC01445	ENST00000654826.1	n.138-2838T>C		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.133 AC: 5503 AN: 41510

American (AMR) AF: 0.311 AC: 4737 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3468

East Asian (EAS) AF: 0.386 AC: 1991 AN: 5154

South Asian (SAS) AF: 0.375 AC: 1803 AN: 4808

European-Finnish (FIN) AF: 0.380 AC: 4017 AN: 10566

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21899 AN: 67954

Other (OTH) AF: 0.272 AC: 576 AN: 2114

Alfa AF: 0.318 Hom.: 4541

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
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs4245562; hg19: chr7-54403985;