chr4-128425815-T-C

Variant names:

• chr4-128425815-T-C
• rs11098966
• ENST00000505133.5:n.531-34512T>C

Variant summary

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

The ENST00000505133.5(LINC02615):​n.531-34512T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,844 control chromosomes in the GnomAD database, including 9,437 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 0.35 (9437 hom., cov: 31)
• Consequence: LINC02615 ENST00000505133.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494
• Publications: 5 publications found

Genes affected

LINC02615 (HGNC:53402): (long intergenic non-protein coding RNA 2615)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.449 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
LINC02615	ENST00000505133.5	n.531-34512T>C		intron_variant	Intron 3 of 4	3
LINC02615	ENST00000509834.6	n.349-44235T>C		intron_variant	Intron 3 of 4	5
LINC02615	ENST00000816105.1	n.159-40793T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52890 AN: 151726 Hom.: 9439 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.348 AC: 52916 AN: 151844 Hom.: 9437 Cov.: 31 AF XY: 0.354 AC XY: 26250 AN XY: 74202

African (AFR) AF: 0.374 AC: 15467 AN: 41402

American (AMR) AF: 0.458 AC: 6976 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3468

East Asian (EAS) AF: 0.273 AC: 1409 AN: 5170

South Asian (SAS) AF: 0.433 AC: 2082 AN: 4804

European-Finnish (FIN) AF: 0.317 AC: 3344 AN: 10540

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21069 AN: 67910

Other (OTH) AF: 0.368 AC: 776 AN: 2106

Alfa AF: 0.330 Hom.: 22880

Bravo AF: 0.354

Asia WGS AF: 0.339 AC: 1181 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.7
DANN	Benign	0.83
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs11098966; hg19: chr4-129346970;