6-169164940-C-A

Variant names:

• chr6-169164940-C-A
• rs6910183
• ENST00000715775.1:n.398-3726G>T

Variant summary

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

The ENST00000715775.1(LINC01615):​n.398-3726G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,176 control chromosomes in the GnomAD database, including 43,900 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 0.76 (43900 hom., cov: 33)
• Consequence: LINC01615 ENST00000715775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 6 publications found

Genes affected

LINC01615 (HGNC:51898): (long intergenic non-protein coding RNA 1615)

ENSG00000308177 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715775.1. 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
	LINC01615	ENST00000715775.1		n.398-3726G>T		intron	N/A
	LINC01615	ENST00000831997.1		n.174-6484G>T		intron	N/A
	LINC01615	ENST00000831998.1		n.294-6484G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115041 AN: 152058 Hom.: 43867 Cov.: 33

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.756 AC: 115119 AN: 152176 Hom.: 43900 Cov.: 33 AF XY: 0.757 AC XY: 56293 AN XY: 74410

African (AFR) AF: 0.698 AC: 28961 AN: 41482

American (AMR) AF: 0.702 AC: 10729 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2679 AN: 3468

East Asian (EAS) AF: 0.722 AC: 3745 AN: 5184

South Asian (SAS) AF: 0.641 AC: 3091 AN: 4820

European-Finnish (FIN) AF: 0.853 AC: 9046 AN: 10610

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54315 AN: 68004

Other (OTH) AF: 0.739 AC: 1562 AN: 2114

Alfa AF: 0.778 Hom.: 130071

Bravo AF: 0.743

Asia WGS AF: 0.656 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.034
DANN	Benign	0.29
PhyloP100		-2.3

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: rs6910183;

hg19: chr6-169565035;