rs10501206

chr11-38678280-A-G

Variant summary

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

The ENST00000649890.1(LINC01493):n.535-69A>G 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 0.905 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03

Genes affected

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

LOC105376635 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105376635	XR_007062971.1	n.416-69A>G		intron_variant, non_coding_transcript_variant
LOC105376635	XR_007062967.1	n.1024-69A>G		intron_variant, non_coding_transcript_variant
LOC105376635	XR_007062969.1	n.597-69A>G		intron_variant, non_coding_transcript_variant
LOC105376635	XR_931205.3	n.952-69A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01493	ENST00000649890.1	n.535-69A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.987

Gnomad4 NFE AF: 0.993

Gnomad4 OTH AF: 0.937

Alfa AF: 0.962 Hom.: 27685

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501206; hg19: chr11-38699830;