ENST00000649890.1:n.630A>G

Variant names:

• chr11-38678444-A-G
• rs10501207
• ENST00000649890.1:n.630A>G

Variant summary

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

The ENST00000649890.1(LINC01493):​n.630A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.905 in 152,150 control chromosomes in the GnomAD database, including 63,478 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 (63478 hom., cov: 32)
• Consequence: LINC01493 ENST00000649890.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649890.1. 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
	LOC105376635	NR_188550.1		n.605A>G		non_coding_transcript_exon	Exon 4 of 7
	LOC105376635	NR_188551.1		n.511A>G		non_coding_transcript_exon	Exon 4 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01493	ENST00000649890.1		n.630A>G		non_coding_transcript_exon	Exon 4 of 7
	LINC01493	ENST00000759813.1		n.185A>G		non_coding_transcript_exon	Exon 3 of 6
	LINC01493	ENST00000759814.1		n.529A>G		non_coding_transcript_exon	Exon 5 of 8

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137688 AN: 152032 Hom.: 63465 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.955

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: 137743 AN: 152150 Hom.: 63478 Cov.: 32 AF XY: 0.906 AC XY: 67371 AN XY: 74386

African (AFR) AF: 0.723 AC: 29965 AN: 41454

American (AMR) AF: 0.955 AC: 14591 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3380 AN: 3472

East Asian (EAS) AF: 0.831 AC: 4290 AN: 5162

South Asian (SAS) AF: 0.899 AC: 4332 AN: 4818

European-Finnish (FIN) AF: 0.987 AC: 10483 AN: 10616

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

European-Non Finnish (NFE) AF: 0.993 AC: 67532 AN: 68026

Other (OTH) AF: 0.937 AC: 1980 AN: 2114

Alfa AF: 0.960 Hom.: 14320

Bravo AF: 0.897

Asia WGS AF: 0.876 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.63
DANN	Benign	0.52
PhyloP100		-0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10501207;

hg19: chr11-38699994;