chr2-65635244-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420724.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03050	ENST00000420724.1	TSL:1	n.63+4871C>T		intron	N/A
	LINC02934	ENST00000377977.3	TSL:2	n.863-56538G>A		intron	N/A
	LINC02934	ENST00000606978.5	TSL:5	n.456-56538G>A		intron	N/A

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

African (AFR) AF: 0.168 AC: 6992 AN: 41498

American (AMR) AF: 0.129 AC: 1975 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0640 AC: 222 AN: 3470

East Asian (EAS) AF: 0.173 AC: 894 AN: 5182

South Asian (SAS) AF: 0.274 AC: 1321 AN: 4816

European-Finnish (FIN) AF: 0.147 AC: 1553 AN: 10590

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0991 AC: 6739 AN: 67990

Other (OTH) AF: 0.110 AC: 233 AN: 2114

Alfa AF: 0.111 Hom.: 4651

Bravo AF: 0.131

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1457451; hg19: chr2-65862378;