rs10889990

Positions:

• chr1-72779485-G-A

Variant summary

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

The ENST00000418078.3(LINC02796):​n.409-622G>A 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 0.0833 in 152,070 control chromosomes in the GnomAD database, including 1,492 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 0.083 (1492 hom., cov: 32)
• Consequence: LINC02796 ENST00000418078.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

Genes affected

LINC02796 (HGNC:27918): (long intergenic non-protein coding RNA 2796)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02796	XR_007066169.1	n.761+1128G>A		intron_variant, non_coding_transcript_variant
LINC02796	XR_007066168.1	n.761+1128G>A		intron_variant, non_coding_transcript_variant
LINC02796	XR_007066170.1	n.761+1128G>A		intron_variant, non_coding_transcript_variant
LINC02796	XR_947509.4	n.761+1128G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02796	ENST00000418078.3	n.409-622G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000668734.1	n.262-12798C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12616 AN: 151952 Hom.: 1476 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.00684

Gnomad FIN AF: 0.00887

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0833 AC: 12670 AN: 152070 Hom.: 1492 Cov.: 32 AF XY: 0.0798 AC XY: 5929 AN XY: 74342

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.0352

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.00684

Gnomad4 FIN AF: 0.00887

Gnomad4 NFE AF: 0.0104

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0463 Hom.: 212

Bravo AF: 0.0946

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10889990; hg19: chr1-73245168;