chr4-169959732-G-A

Variant names:

• chr4-169959732-G-A
• rs11723530
• ENST00000508313.4:n.97+16084C>T

Variant summary

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

The ENST00000508313.4(LINC02275):​n.97+16084C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,890 control chromosomes in the GnomAD database, including 13,519 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 0.40 (13519 hom., cov: 31)
• Consequence: LINC02275 ENST00000508313.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76
• Publications: 7 publications found

Genes affected

LINC02275 (HGNC:53191): (long intergenic non-protein coding RNA 2275)

ENSG00000251200 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02275	NR_037878.1	n.87+16084C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02275	ENST00000508313.4	n.97+16084C>T		intron_variant	Intron 1 of 4	2
ENSG00000251200	ENST00000509956.1	n.250-3403G>A		intron_variant	Intron 1 of 1	2
LINC02275	ENST00000657085.2	n.89+16084C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60366 AN: 151772 Hom.: 13509 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.0481

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.398 AC: 60387 AN: 151890 Hom.: 13519 Cov.: 31 AF XY: 0.396 AC XY: 29405 AN XY: 74226

African (AFR) AF: 0.212 AC: 8771 AN: 41418

American (AMR) AF: 0.451 AC: 6874 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 2000 AN: 3470

East Asian (EAS) AF: 0.0486 AC: 251 AN: 5160

South Asian (SAS) AF: 0.374 AC: 1801 AN: 4816

European-Finnish (FIN) AF: 0.484 AC: 5088 AN: 10512

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.504 AC: 34220 AN: 67954

Other (OTH) AF: 0.407 AC: 855 AN: 2102

Alfa AF: 0.466 Hom.: 74278

Bravo AF: 0.381

Asia WGS AF: 0.204 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.028
DANN	Benign	0.24
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs11723530; hg19: chr4-170880883;