chr6-169164779-A-C

Variant names:

• chr6-169164779-A-C
• rs2095019
• ENST00000715775.1:n.398-3565T>G

Variant summary

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

The ENST00000715775.1(LINC01615):​n.398-3565T>G 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 152,080 control chromosomes in the GnomAD database, including 43,858 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 (43858 hom., cov: 32)
• Consequence: LINC01615 ENST00000715775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• 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=-0.96).
• 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.398-3565T>G		intron	N/A
	LINC01615	ENST00000831997.1		n.174-6323T>G		intron	N/A
	LINC01615	ENST00000831998.1		n.294-6323T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114943 AN: 151962 Hom.: 43824 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.756 AC: 115022 AN: 152080 Hom.: 43858 Cov.: 32 AF XY: 0.757 AC XY: 56246 AN XY: 74346

African (AFR) AF: 0.698 AC: 28942 AN: 41480

American (AMR) AF: 0.702 AC: 10718 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2677 AN: 3468

East Asian (EAS) AF: 0.722 AC: 3713 AN: 5146

South Asian (SAS) AF: 0.642 AC: 3089 AN: 4814

European-Finnish (FIN) AF: 0.853 AC: 9034 AN: 10588

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

European-Non Finnish (NFE) AF: 0.799 AC: 54297 AN: 67998

Other (OTH) AF: 0.741 AC: 1564 AN: 2110

Alfa AF: 0.762 Hom.: 7900

Bravo AF: 0.744

Asia WGS AF: 0.657 AC: 2285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.26
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2095019; hg19: chr6-169564874;