13-63978690-C-T

Variant names:

• chr13-63978690-C-T
• rs7993570
• ENST00000650541.1:n.1242+11406G>A

Variant summary

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

The ENST00000650541.1(LINC00355):​n.1242+11406G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,934 control chromosomes in the GnomAD database, including 25,367 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 0.56 (25367 hom., cov: 32)
• Consequence: LINC00355 ENST00000650541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650541.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00355	ENST00000650541.1		n.1242+11406G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84558 AN: 151814 Hom.: 25359 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.557 AC: 84593 AN: 151934 Hom.: 25367 Cov.: 32 AF XY: 0.557 AC XY: 41362 AN XY: 74256

African (AFR) AF: 0.320 AC: 13285 AN: 41454

American (AMR) AF: 0.574 AC: 8763 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2162 AN: 3472

East Asian (EAS) AF: 0.665 AC: 3430 AN: 5156

South Asian (SAS) AF: 0.503 AC: 2417 AN: 4802

European-Finnish (FIN) AF: 0.706 AC: 7453 AN: 10550

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45135 AN: 67926

Other (OTH) AF: 0.568 AC: 1199 AN: 2110

Alfa AF: 0.615 Hom.: 4042

Bravo AF: 0.538

Asia WGS AF: 0.577 AC: 1999 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.33
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs7993570; hg19: chr13-64552823;