rs754059

chr10-118810998-G-Achr10-118810998-G-Cchr10-118810998-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663084.1(LINC03036):n.397-23956C>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 0.626 in 152,152 control chromosomes in the GnomAD database, including 29,954 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 0.63 (29954 hom., cov: 34)
• Consequence: LINC03036 ENST00000663084.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03036	ENST00000663084.1	n.397-23956C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95211 AN: 152034 Hom.: 29927 Cov.: 34

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.626 AC: 95291 AN: 152152 Hom.: 29954 Cov.: 34 AF XY: 0.624 AC XY: 46384 AN XY: 74366

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.647

Alfa AF: 0.609 Hom.: 13363

Bravo AF: 0.632

Asia WGS AF: 0.600 AC: 2082 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.7
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754059; hg19: chr10-120570510;