rs275897

Positions:

• chr13-63892457-C-A
• chr13-63892457-C-T

Variant summary

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

The ENST00000650541.1(LINC00355):​n.1243-38698G>T 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 0.248 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00355	ENST00000650541.1	n.1243-38698G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0938

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.224

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275897; hg19: chr13-64466590;