ENST00000649890.1:n.535-69A>G

Variant names:

• chr11-38678280-A-G
• rs10501206
• ENST00000649890.1:n.535-69A>G

Variant summary

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

The ENST00000649890.1(LINC01493):​n.535-69A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,206 control chromosomes in the GnomAD database, including 63,495 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 0.91 (63495 hom., cov: 33)
• Consequence: LINC01493 ENST00000649890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03
• Publications: 1 publications found

Genes affected

LINC01493 (HGNC:51150): (long intergenic non-protein coding RNA 1493)

LOC105376635 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376635	NR_188550.1	n.510-69A>G		intron_variant	Intron 3 of 6
LOC105376635	NR_188551.1	n.416-69A>G		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01493	ENST00000649890.1	n.535-69A>G		intron_variant	Intron 3 of 6
LINC01493	ENST00000759813.1	n.165-144A>G		intron_variant	Intron 2 of 5
LINC01493	ENST00000759814.1	n.434-69A>G		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137740 AN: 152090 Hom.: 63482 Cov.: 33

Gnomad AFR AF: 0.724

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.905 AC: 137794 AN: 152206 Hom.: 63495 Cov.: 33 AF XY: 0.906 AC XY: 67403 AN XY: 74422

African (AFR) AF: 0.723 AC: 29990 AN: 41474

American (AMR) AF: 0.955 AC: 14592 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3379 AN: 3470

East Asian (EAS) AF: 0.830 AC: 4300 AN: 5178

South Asian (SAS) AF: 0.899 AC: 4341 AN: 4828

European-Finnish (FIN) AF: 0.987 AC: 10480 AN: 10614

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67540 AN: 68034

Other (OTH) AF: 0.937 AC: 1982 AN: 2116

Alfa AF: 0.964 Hom.: 31410

Bravo AF: 0.897

Asia WGS AF: 0.877 AC: 3049 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	8.7
DANN	Benign	0.62
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs10501206; hg19: chr11-38699830;