10-101238760-C-T

Variant names:

• chr10-101238760-C-T
• rs1052895
• ENST00000546988.3:n.1241C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000546988.3(LBX1-AS1):​n.1241C>T 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 0.0227 in 152,334 control chromosomes in the GnomAD database, including 59 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 0.023 (59 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LBX1-AS1 ENST00000546988.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30
• Publications: 1 publications found

Genes affected

LBX1-AS1 (HGNC:48678): (LBX1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0227 (3459/152334) while in subpopulation NFE AF = 0.0309 (2101/68018). AF 95% confidence interval is 0.0298. There are 59 homozygotes in GnomAd4. There are 1753 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 59 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LBX1-AS1	NR_029380.1	n.1224C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LBX1-AS1	ENST00000546988.3	n.1241C>T		non_coding_transcript_exon_variant	Exon 3 of 3	1
LBX1-AS1	ENST00000430651.2	n.2465C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2
LBX1-AS1	ENST00000456391.2	n.828C>T		non_coding_transcript_exon_variant	Exon 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0227 AC: 3459 AN: 152216 Hom.: 59 Cov.: 33

Gnomad AFR AF: 0.00473

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0208

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00703

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0177

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0227 AC: 3459 AN: 152334 Hom.: 59 Cov.: 33 AF XY: 0.0235 AC XY: 1753 AN XY: 74482

African (AFR) AF: 0.00471 AC: 196 AN: 41592

American (AMR) AF: 0.0208 AC: 318 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00704 AC: 34 AN: 4830

European-Finnish (FIN) AF: 0.0701 AC: 743 AN: 10602

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0309 AC: 2101 AN: 68018

Other (OTH) AF: 0.0175 AC: 37 AN: 2114

Alfa AF: 0.0211 Hom.: 13

Bravo AF: 0.0181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	19
DANN	Benign	0.73
PhyloP100		2.3
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1052895; hg19: chr10-102998517;