rs6856616

Variant names:

• chr4-38323415-T-C
• rs6856616
• ENST00000503465.2:n.234+35269T>C

Variant summary

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

The ENST00000503465.2(LINC02513):​n.234+35269T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,242 control chromosomes in the GnomAD database, including 2,469 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 0.15 (2469 hom., cov: 33)
• Consequence: LINC02513 ENST00000503465.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.764
• Publications: 31 publications found

Genes affected

LINC02513 (HGNC:53502): (long intergenic non-protein coding RNA 2513)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 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
LINC02513	ENST00000503465.2	n.234+35269T>C		intron_variant	Intron 2 of 3	2
LINC02513	ENST00000757609.1	n.234+35269T>C		intron_variant	Intron 2 of 4
LINC02513	ENST00000757610.1	n.215+35269T>C		intron_variant	Intron 1 of 2
LINC02513	ENST00000757611.1	n.213+35269T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22646 AN: 152124 Hom.: 2469 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0675

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.149 AC: 22659 AN: 152242 Hom.: 2469 Cov.: 33 AF XY: 0.150 AC XY: 11142 AN XY: 74434

African (AFR) AF: 0.290 AC: 12048 AN: 41506

American (AMR) AF: 0.164 AC: 2506 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1151 AN: 5170

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4828

European-Finnish (FIN) AF: 0.0263 AC: 279 AN: 10620

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0674 AC: 4587 AN: 68026

Other (OTH) AF: 0.146 AC: 308 AN: 2112

Alfa AF: 0.0956 Hom.: 4337

Bravo AF: 0.161

Asia WGS AF: 0.194 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.8
DANN	Benign	0.68
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs6856616; hg19: chr4-38325036;