rs17403780

Variant names:

• chr1-191970658-T-A
• rs17403780
• ENST00000430776.2:n.394+5245T>A

Variant summary

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

The ENST00000430776.2(LINC02770):​n.394+5245T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 152,266 control chromosomes in the GnomAD database, including 272 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 0.051 (272 hom., cov: 32)
• Consequence: LINC02770 ENST00000430776.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 2 publications found

Genes affected

LINC02770 (HGNC:54290): (long intergenic non-protein coding RNA 2770)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02770	NR_186758.1	n.807+5245T>A		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02770	ENST00000430776.2	n.394+5245T>A		intron_variant	Intron 3 of 5	1
LINC02770	ENST00000664489.1	n.353+5245T>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 7747 AN: 152148 Hom.: 272 Cov.: 32

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0476

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0194

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0813

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0508 AC: 7742 AN: 152266 Hom.: 272 Cov.: 32 AF XY: 0.0484 AC XY: 3605 AN XY: 74452

African (AFR) AF: 0.0147 AC: 611 AN: 41582

American (AMR) AF: 0.0475 AC: 726 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0334 AC: 116 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.0193 AC: 93 AN: 4830

European-Finnish (FIN) AF: 0.0432 AC: 459 AN: 10614

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0813 AC: 5528 AN: 68000

Other (OTH) AF: 0.0469 AC: 99 AN: 2112

Alfa AF: 0.0581 Hom.: 31

Bravo AF: 0.0501

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.52
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs17403780; hg19: chr1-191939788;