4-137981717-G-A

Variant names:

• chr4-137981717-G-A
• rs6825001
• ENST00000655176.1:n.660+29188G>A

Variant summary

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

The ENST00000655176.1(ENSG00000287144):​n.660+29188G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 151,704 control chromosomes in the GnomAD database, including 58,751 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 0.88 (58751 hom., cov: 31)
• Consequence: ENSG00000287144 ENST00000655176.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 1 publications found

Genes affected

ENSG00000287144 (HGNC:):

LINC00616 (HGNC:44065): (long intergenic non-protein coding RNA 616)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655176.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287144	ENST00000655176.1		n.660+29188G>A		intron	N/A
	LINC00616	ENST00000656980.1		n.844-2952C>T		intron	N/A
	LINC00616	ENST00000661963.1		n.806-2952C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133196 AN: 151586 Hom.: 58713 Cov.: 31

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.879 AC: 133295 AN: 151704 Hom.: 58751 Cov.: 31 AF XY: 0.882 AC XY: 65357 AN XY: 74086

African (AFR) AF: 0.804 AC: 33243 AN: 41354

American (AMR) AF: 0.918 AC: 13983 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3246 AN: 3464

East Asian (EAS) AF: 0.943 AC: 4860 AN: 5156

South Asian (SAS) AF: 0.958 AC: 4605 AN: 4808

European-Finnish (FIN) AF: 0.922 AC: 9659 AN: 10478

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60743 AN: 67900

Other (OTH) AF: 0.895 AC: 1884 AN: 2106

Alfa AF: 0.894 Hom.: 149419

Bravo AF: 0.873

Asia WGS AF: 0.908 AC: 3158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.92
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs6825001; hg19: chr4-138902871;