chr10-118931320-G-A

Variant names:

• chr10-118931320-G-A
• rs10886342
• ENST00000663084.1:n.265-65002C>T

Variant summary

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

The ENST00000663084.1(LINC03036):​n.265-65002C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,960 control chromosomes in the GnomAD database, including 6,198 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 0.27 (6198 hom., cov: 32)
• Consequence: LINC03036 ENST00000663084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 5 publications found

Genes affected

LINC03036 (HGNC:56220): (long intergenic non-protein coding RNA 3036)

ENSG00000294178 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03036	NR_186540.1	n.292-65002C>T		intron_variant	Intron 2 of 3
LINC03036	NR_186541.1	n.304-9900C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03036	ENST00000663084.1	n.265-65002C>T		intron_variant	Intron 2 of 3
ENSG00000294178	ENST00000721698.1	n.131-9900C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41072 AN: 151842 Hom.: 6196 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.270 AC: 41097 AN: 151960 Hom.: 6198 Cov.: 32 AF XY: 0.273 AC XY: 20303 AN XY: 74286

African (AFR) AF: 0.143 AC: 5948 AN: 41500

American (AMR) AF: 0.363 AC: 5535 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3464

East Asian (EAS) AF: 0.438 AC: 2265 AN: 5174

South Asian (SAS) AF: 0.265 AC: 1277 AN: 4826

European-Finnish (FIN) AF: 0.349 AC: 3680 AN: 10542

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.300 AC: 20388 AN: 67898

Other (OTH) AF: 0.292 AC: 614 AN: 2104

Alfa AF: 0.295 Hom.: 28759

Bravo AF: 0.273

Asia WGS AF: 0.325 AC: 1123 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.2
DANN	Benign	0.63
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10886342; hg19: chr10-120690832;