rs694444

Variant names:

• chr13-63900046-A-G
• rs694444
• ENST00000650541.1:n.1243-46287T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-63900046-A-G
• chr13-63900046-A-T

Variant summary

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

The ENST00000650541.1(LINC00355):​n.1243-46287T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 151,888 control chromosomes in the GnomAD database, including 49,813 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 0.81 (49813 hom., cov: 31)
• Consequence: LINC00355 ENST00000650541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 4 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 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.1243-46287T>C		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122697 AN: 151770 Hom.: 49754 Cov.: 31

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.809 AC: 122816 AN: 151888 Hom.: 49813 Cov.: 31 AF XY: 0.810 AC XY: 60129 AN XY: 74206

African (AFR) AF: 0.853 AC: 35375 AN: 41466

American (AMR) AF: 0.815 AC: 12414 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2715 AN: 3464

East Asian (EAS) AF: 0.753 AC: 3880 AN: 5150

South Asian (SAS) AF: 0.716 AC: 3446 AN: 4814

European-Finnish (FIN) AF: 0.852 AC: 9016 AN: 10588

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53389 AN: 67856

Other (OTH) AF: 0.796 AC: 1679 AN: 2110

Alfa AF: 0.791 Hom.: 191224

Bravo AF: 0.806

Asia WGS AF: 0.766 AC: 2664 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.39
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs694444; hg19: chr13-64474179;