rs10519663

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-29687136-A-C
• chr15-29687136-A-G
• chr15-29687136-A-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841149.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCIIAR	ENST00000841149.1		n.326+9720A>C		intron	N/A

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 v4.9

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;