15-29687136-A-C

Variant names:

• chr15-29687136-A-C
• rs10519663
• XR_932029.3:n.354T>G

Variant summary

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

The XR_932029.3(LOC105370743):​n.354T>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 0.11 in 152,286 control chromosomes in the GnomAD database, including 984 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 0.11 (984 hom., cov: 33)
• Consequence: LOC105370743 XR_932029.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 5 publications found

Genes affected

LOC105370743 (HGNC:):

LCIIAR (HGNC:56346): (lung cancer immune cell infiltration associated lncRNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370743	XR_932029.3	n.354T>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105370743	XR_932031.3	n.354T>G		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105370743	XR_932032.2	n.-183T>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LCIIAR	ENST00000841149.1	n.326+9720A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16701 AN: 152168 Hom.: 978 Cov.: 33

Gnomad AFR AF: 0.0770

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0927

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.110 AC: 16718 AN: 152286 Hom.: 984 Cov.: 33 AF XY: 0.111 AC XY: 8286 AN XY: 74468

African (AFR) AF: 0.0773 AC: 3214 AN: 41566

American (AMR) AF: 0.159 AC: 2427 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3470

East Asian (EAS) AF: 0.120 AC: 623 AN: 5180

South Asian (SAS) AF: 0.220 AC: 1061 AN: 4824

European-Finnish (FIN) AF: 0.0927 AC: 984 AN: 10612

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7634 AN: 68028

Other (OTH) AF: 0.131 AC: 277 AN: 2112

Alfa AF: 0.115 Hom.: 2123

Bravo AF: 0.111

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.40
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs10519663; hg19: chr15-29979340;