chr13-63892457-C-A

Variant names:

• chr13-63892457-C-A
• rs275897
• ENST00000650541.1:n.1243-38698G>T

Variant summary

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

The ENST00000650541.1(LINC00355):​n.1243-38698G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,142 control chromosomes in the GnomAD database, including 7,339 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 0.25 (7339 hom., cov: 31)
• Consequence: LINC00355 ENST00000650541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 1 publications found

Genes affected

LINC00355 (HGNC:27061): (long intergenic non-protein coding RNA 355)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00355	ENST00000650541.1	n.1243-38698G>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37448 AN: 151032 Hom.: 7315 Cov.: 31

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0935

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.248 AC: 37530 AN: 151142 Hom.: 7339 Cov.: 31 AF XY: 0.249 AC XY: 18411 AN XY: 73792

African (AFR) AF: 0.539 AC: 22247 AN: 41246

American (AMR) AF: 0.234 AC: 3541 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 650 AN: 3462

East Asian (EAS) AF: 0.0938 AC: 483 AN: 5152

South Asian (SAS) AF: 0.220 AC: 1057 AN: 4810

European-Finnish (FIN) AF: 0.133 AC: 1377 AN: 10386

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.112 AC: 7561 AN: 67662

Other (OTH) AF: 0.224 AC: 469 AN: 2098

Alfa AF: 0.0775 Hom.: 149

Bravo AF: 0.265

Asia WGS AF: 0.191 AC: 659 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.15
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs275897; hg19: chr13-64466590;