chr4-128537478-T-C

Variant names:

• chr4-128537478-T-C
• rs983158
• ENST00000816105.1:n.568-19512T>C

Variant summary

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

The ENST00000816105.1(LINC02615):​n.568-19512T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,266 control chromosomes in the GnomAD database, including 2,134 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 0.16 (2134 hom., cov: 33)
• Consequence: LINC02615 ENST00000816105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816105.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02615	ENST00000816105.1		n.568-19512T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24161 AN: 152148 Hom.: 2139 Cov.: 33

Gnomad AFR AF: 0.0818

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.159 AC: 24154 AN: 152266 Hom.: 2134 Cov.: 33 AF XY: 0.161 AC XY: 12016 AN XY: 74448

African (AFR) AF: 0.0817 AC: 3394 AN: 41552

American (AMR) AF: 0.147 AC: 2250 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3468

East Asian (EAS) AF: 0.138 AC: 718 AN: 5192

South Asian (SAS) AF: 0.268 AC: 1292 AN: 4828

European-Finnish (FIN) AF: 0.186 AC: 1974 AN: 10598

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13165 AN: 68014

Other (OTH) AF: 0.170 AC: 359 AN: 2114

Alfa AF: 0.135 Hom.: 338

Bravo AF: 0.148

Asia WGS AF: 0.182 AC: 632 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.9
DANN	Benign	0.87
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs983158;

hg19: chr4-129458633;