rs885170

Positions:

• chr13-34623652-A-G
• chr13-34623652-A-T

Variant summary

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

The NR_047036.1(LINC00457):​n.81+16953T>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 0.183 in 151,586 control chromosomes in the GnomAD database, including 2,574 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 0.18 (2574 hom., cov: 30)
• Consequence: LINC00457 NR_047036.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

LINC00457 (HGNC:42805): (long intergenic non-protein coding RNA 457)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00457	NR_047036.1	n.81+16953T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00457	ENST00000440160.1	n.81+16953T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000606365.1	n.183+47348T>C		intron_variant, non_coding_transcript_variant		5
LINC00457	ENST00000660916.1	n.199+16953T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27748 AN: 151468 Hom.: 2572 Cov.: 30

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.183 AC: 27777 AN: 151586 Hom.: 2574 Cov.: 30 AF XY: 0.181 AC XY: 13395 AN XY: 74054

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.194

Alfa AF: 0.184 Hom.: 2465

Bravo AF: 0.187

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.059
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs885170; hg19: chr13-35197789;