rs10484212

Variant names:

• chr4-37109858-A-T
• rs10484212
• ENST00000501725.4:n.224+502A>T

Variant summary

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

The ENST00000501725.4(LINC02616):​n.224+502A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,968 control chromosomes in the GnomAD database, including 9,003 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 0.28 (9003 hom., cov: 32)
• Consequence: LINC02616 ENST00000501725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 1 publications found

Genes affected

LINC02616 (HGNC:54078): (long intergenic non-protein coding RNA 2616)

ENSG00000293926 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928721	NR_188345.1	n.1040+502A>T		intron_variant	Intron 5 of 5
LOC101928721	NR_188346.1	n.652+502A>T		intron_variant	Intron 3 of 3
LOC101928721	NR_188347.1	n.1249+502A>T		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02616	ENST00000501725.4	n.224+502A>T		intron_variant	Intron 3 of 3	3
LINC02616	ENST00000508199.5	n.133+502A>T		intron_variant	Intron 2 of 2	3
LINC02616	ENST00000652451.1	n.1468+502A>T		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41748 AN: 151850 Hom.: 8975 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.0893

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.275 AC: 41850 AN: 151968 Hom.: 9003 Cov.: 32 AF XY: 0.275 AC XY: 20424 AN XY: 74312

African (AFR) AF: 0.586 AC: 24238 AN: 41388

American (AMR) AF: 0.324 AC: 4938 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 451 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2038 AN: 5154

South Asian (SAS) AF: 0.0902 AC: 435 AN: 4822

European-Finnish (FIN) AF: 0.135 AC: 1432 AN: 10590

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7639 AN: 67978

Other (OTH) AF: 0.246 AC: 518 AN: 2108

Alfa AF: 0.203 Hom.: 692

Bravo AF: 0.308

Asia WGS AF: 0.260 AC: 903 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	2.0
DANN	Benign	0.30
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs10484212; hg19: chr4-37111480;