rs10787879

Positions:

• chr10-118928058-C-A
• chr10-118928058-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000663084.1(LINC03036):​n.265-61740G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,152 control chromosomes in the GnomAD database, including 39,567 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 0.71 (39567 hom., cov: 32)
• Consequence: LINC03036 ENST00000663084.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03036	ENST00000663084.1	n.265-61740G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108122 AN: 152034 Hom.: 39541 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.711 AC: 108199 AN: 152152 Hom.: 39567 Cov.: 32 AF XY: 0.714 AC XY: 53078 AN XY: 74374

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.712

Alfa AF: 0.771 Hom.: 73932

Bravo AF: 0.701

Asia WGS AF: 0.734 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	17
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10787879; hg19: chr10-120687570;