rs4708273

Variant names:

• chr6-76554566-T-A
• rs4708273
• ENST00000455554.2:n.217-31762A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-76554566-T-A
• chr6-76554566-T-C
• chr6-76554566-T-G

Variant summary

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

The ENST00000455554.2(LINC02540):​n.217-31762A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 152,084 control chromosomes in the GnomAD database, including 37,353 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 0.69 (37353 hom., cov: 32)
• Consequence: LINC02540 ENST00000455554.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 3 publications found

Genes affected

LINC02540 (HGNC:53573): (long intergenic non-protein coding RNA 2540)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02540	NR_149101.1	n.217-31762A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02540	ENST00000455554.2	n.217-31762A>T		intron_variant	Intron 2 of 2	3
LINC02540	ENST00000653622.1	n.154-31762A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105263 AN: 151966 Hom.: 37302 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.693 AC: 105372 AN: 152084 Hom.: 37353 Cov.: 32 AF XY: 0.693 AC XY: 51535 AN XY: 74344

African (AFR) AF: 0.844 AC: 35030 AN: 41514

American (AMR) AF: 0.704 AC: 10747 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1931 AN: 3472

East Asian (EAS) AF: 0.770 AC: 3974 AN: 5160

South Asian (SAS) AF: 0.701 AC: 3386 AN: 4828

European-Finnish (FIN) AF: 0.623 AC: 6581 AN: 10568

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41604 AN: 67964

Other (OTH) AF: 0.658 AC: 1383 AN: 2102

Alfa AF: 0.660 Hom.: 4197

Bravo AF: 0.704

Asia WGS AF: 0.738 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.61
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs4708273; hg19: chr6-77264283;