rs1457451

Variant names:

• chr2-65635244-G-A
• rs1457451
• ENST00000420724.1:n.63+4871C>T

Variant summary

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

The ENST00000420724.1(LINC03050):​n.63+4871C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,148 control chromosomes in the GnomAD database, including 1,436 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 0.13 (1436 hom., cov: 32)
• Consequence: LINC03050 ENST00000420724.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

LINC03050 (HGNC:56283): (long intergenic non-protein coding RNA 3050)

LINC02934 (HGNC:55913): (long intergenic non-protein coding RNA 2934)

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 (SAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03050	ENST00000420724.1	n.63+4871C>T		intron_variant	Intron 1 of 3	1
LINC02934	ENST00000377977.3	n.863-56538G>A		intron_variant	Intron 4 of 4	2
LINC02934	ENST00000606978.5	n.456-56538G>A		intron_variant	Intron 4 of 9	5

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19954 AN: 152032 Hom.: 1435 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.131 AC: 19966 AN: 152148 Hom.: 1436 Cov.: 32 AF XY: 0.136 AC XY: 10120 AN XY: 74410

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0640

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.0991

Gnomad4 OTH AF: 0.110

Alfa AF: 0.107 Hom.: 2100

Bravo AF: 0.131

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1457451; hg19: chr2-65862378;