rs17066681

Variant names:

• chr6-137652212-G-A
• rs17066681
• ENST00000746620.1:n.105+4221G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-137652212-G-A
• chr6-137652212-G-T

Variant summary

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

The ENST00000746620.1(LINC03004):​n.105+4221G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0891 in 152,228 control chromosomes in the GnomAD database, including 646 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 0.089 (646 hom., cov: 31)
• Consequence: LINC03004 ENST00000746620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690
• Publications: 5 publications found

Genes affected

LINC03004 (HGNC:56128): (long intergenic non-protein coding RNA 3004)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746620.1. 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
	LINC03004	ENST00000746620.1		n.105+4221G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0890 AC: 13543 AN: 152110 Hom.: 642 Cov.: 31

Gnomad AFR AF: 0.0936

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.0835

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.0890

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

GnomAD4 genome AF: 0.0891 AC: 13558 AN: 152228 Hom.: 646 Cov.: 31 AF XY: 0.0893 AC XY: 6644 AN XY: 74432

African (AFR) AF: 0.0934 AC: 3878 AN: 41542

American (AMR) AF: 0.107 AC: 1643 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3464

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5186

South Asian (SAS) AF: 0.0720 AC: 347 AN: 4818

European-Finnish (FIN) AF: 0.0835 AC: 885 AN: 10602

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0880 AC: 5985 AN: 67998

Other (OTH) AF: 0.0885 AC: 187 AN: 2112

Alfa AF: 0.0841 Hom.: 385

Bravo AF: 0.0927

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.67
PhyloP100		0.69

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: rs17066681;

hg19: chr6-137973349;