rs6466707

Variant names:

• chr7-119681521-C-G
• rs6466707
• ENST00000804423.1:n.907G>C

Your query was ambiguous. Multiple possible variants found:

• chr7-119681521-C-G
• chr7-119681521-C-T

Variant summary

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

The ENST00000804423.1(LINC02476):​n.907G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,008 control chromosomes in the GnomAD database, including 35,084 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 0.63 (35084 hom., cov: 32)
• Consequence: LINC02476 ENST00000804423.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 2 publications found

Genes affected

LINC02476 (HGNC:53419): (long intergenic non-protein coding RNA 2476)

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 (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804423.1. 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
	LINC02476	NR_131960.1		n.300-60767G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02476	ENST00000804423.1		n.907G>C		non_coding_transcript_exon	Exon 4 of 4
	LINC02476	ENST00000660268.1		n.216+100763G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96441 AN: 151892 Hom.: 35090 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.634 AC: 96449 AN: 152008 Hom.: 35084 Cov.: 32 AF XY: 0.641 AC XY: 47667 AN XY: 74316

African (AFR) AF: 0.252 AC: 10434 AN: 41438

American (AMR) AF: 0.805 AC: 12287 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2819 AN: 3464

East Asian (EAS) AF: 0.943 AC: 4871 AN: 5168

South Asian (SAS) AF: 0.845 AC: 4073 AN: 4822

European-Finnish (FIN) AF: 0.708 AC: 7484 AN: 10576

Middle Eastern (MID) AF: 0.798 AC: 233 AN: 292

European-Non Finnish (NFE) AF: 0.766 AC: 52052 AN: 67972

Other (OTH) AF: 0.702 AC: 1479 AN: 2106

Alfa AF: 0.543 Hom.: 1797

Bravo AF: 0.625

Asia WGS AF: 0.827 AC: 2872 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.41
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6466707; hg19: chr7-119321575;