13-34623652-A-G

Variant names:

• chr13-34623652-A-G
• rs885170
• ENST00000440160.1:n.81+16953T>C

Variant summary

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

The ENST00000440160.1(LINC00457):​n.81+16953T>C variant causes a intron 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 ENST00000440160.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

Genes affected

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

ENSG00000271901 (HGNC:):

LINC02343 (HGNC:53263): (long intergenic non-protein coding RNA 2343)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00457	NR_047036.1	n.81+16953T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00457	ENST00000440160.1	n.81+16953T>C		intron_variant	Intron 1 of 2	2
ENSG00000271901	ENST00000606365.1	n.183+47348T>C		intron_variant	Intron 1 of 1	5
LINC00457	ENST00000660916.1	n.199+16953T>C		intron_variant	Intron 1 of 2
LINC02343	ENST00000791005.1	n.251-1554A>G		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.207 AC: 8529 AN: 41300

American (AMR) AF: 0.153 AC: 2323 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3466

East Asian (EAS) AF: 0.222 AC: 1133 AN: 5098

South Asian (SAS) AF: 0.105 AC: 500 AN: 4782

European-Finnish (FIN) AF: 0.165 AC: 1736 AN: 10544

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.182 AC: 12348 AN: 67860

Other (OTH) AF: 0.194 AC: 409 AN: 2108

Alfa AF: 0.186 Hom.: 7290

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs885170; hg19: chr13-35197789;