rs6825001

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-137981717-G-A
• chr4-137981717-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287144 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000287144	ENST00000655176.1	n.660+29188G>A		intron_variant	Intron 3 of 8
LINC00616	ENST00000656980.1	n.844-2952C>T		intron_variant	Intron 6 of 6
LINC00616	ENST00000661963.1	n.806-2952C>T		intron_variant	Intron 6 of 6

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

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.918

Gnomad4 ASJ AF: 0.937

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.958

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.895

Alfa AF: 0.896 Hom.: 108249

Bravo AF: 0.873

Asia WGS AF: 0.908 AC: 3158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6825001; hg19: chr4-138902871;