rs10516269

Variant names:

• chr4-13935636-T-G
• rs10516269
• XR_001741382.2:n.7107T>G

Variant summary

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

The XR_001741382.2(LOC107986182):​n.7107T>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 0.135 in 152,184 control chromosomes in the GnomAD database, including 1,595 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 0.13 (1595 hom., cov: 33)
• Consequence: LOC107986182 XR_001741382.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 2 publications found

Genes affected

LOC107986182 (HGNC:):

LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986182	XR_001741382.2	n.7107T>G		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01182	ENST00000503532.1	n.231-24353T>G		intron_variant	Intron 2 of 4	4
LINC01182	ENST00000669061.1	n.714-65185T>G		intron_variant	Intron 4 of 4
LINC01182	ENST00000715489.1	n.727+2291T>G		intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20510 AN: 152066 Hom.: 1597 Cov.: 33

Gnomad AFR AF: 0.0576

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.135 AC: 20514 AN: 152184 Hom.: 1595 Cov.: 33 AF XY: 0.139 AC XY: 10305 AN XY: 74400

African (AFR) AF: 0.0576 AC: 2395 AN: 41552

American (AMR) AF: 0.194 AC: 2970 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 640 AN: 3470

East Asian (EAS) AF: 0.0992 AC: 514 AN: 5184

South Asian (SAS) AF: 0.207 AC: 998 AN: 4824

European-Finnish (FIN) AF: 0.189 AC: 2002 AN: 10568

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10629 AN: 67992

Other (OTH) AF: 0.137 AC: 290 AN: 2116

Alfa AF: 0.149 Hom.: 1647

Bravo AF: 0.130

Asia WGS AF: 0.143 AC: 495 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.77
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10516269; hg19: chr4-13937260;