chr4-37062709-G-T

Variant names:

• chr4-37062709-G-T
• rs13117816
• ENST00000720070.1:n.123-15871G>T

Variant summary

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

The ENST00000720070.1(LINC02616):​n.123-15871G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,086 control chromosomes in the GnomAD database, including 1,994 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 0.14 (1994 hom., cov: 32)
• Consequence: LINC02616 ENST00000720070.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 13 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 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
LINC02616	ENST00000720070.1	n.123-15871G>T		intron_variant	Intron 1 of 5
LINC02616	ENST00000720071.1	n.163-15761G>T		intron_variant	Intron 2 of 5
LINC02616	ENST00000720072.1	n.96-15871G>T		intron_variant	Intron 1 of 3
LINC02616	ENST00000720073.1	n.88-15761G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20795 AN: 151968 Hom.: 1999 Cov.: 32

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.137 AC: 20790 AN: 152086 Hom.: 1994 Cov.: 32 AF XY: 0.144 AC XY: 10716 AN XY: 74334

African (AFR) AF: 0.0538 AC: 2233 AN: 41526

American (AMR) AF: 0.201 AC: 3066 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3470

East Asian (EAS) AF: 0.455 AC: 2341 AN: 5144

South Asian (SAS) AF: 0.282 AC: 1361 AN: 4824

European-Finnish (FIN) AF: 0.166 AC: 1754 AN: 10558

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8844 AN: 67990

Other (OTH) AF: 0.146 AC: 309 AN: 2112

Alfa AF: 0.146 Hom.: 3384

Bravo AF: 0.137

Asia WGS AF: 0.331 AC: 1149 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs13117816; hg19: chr4-37064331;