17-12634661-T-C

Variant names:

• chr17-12634661-T-C
• rs6502198
• ENST00000577679.1:n.406-340T>C

Variant summary

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

The ENST00000577679.1(LINC00670):​n.406-340T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,786 control chromosomes in the GnomAD database, including 15,804 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 0.45 (15804 hom., cov: 31)
• Consequence: LINC00670 ENST00000577679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871
• Publications: 1 publications found

Genes affected

LINC00670 (HGNC:44338): (long intergenic non-protein coding RNA 670)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577679.1. 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
	LINC00670	NR_034144.1		n.419-340T>C		intron	N/A
	LINC00670	NR_034145.1		n.581-340T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00670	ENST00000577679.1	TSL:1	n.406-340T>C		intron	N/A
	LINC00670	ENST00000313495.7	TSL:2	n.767-340T>C		intron	N/A
	LINC00670	ENST00000577863.2	TSL:3	n.608-340T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68540 AN: 151668 Hom.: 15790 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.452 AC: 68602 AN: 151786 Hom.: 15804 Cov.: 31 AF XY: 0.452 AC XY: 33486 AN XY: 74162

African (AFR) AF: 0.461 AC: 19089 AN: 41392

American (AMR) AF: 0.388 AC: 5909 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1456 AN: 3460

East Asian (EAS) AF: 0.632 AC: 3233 AN: 5118

South Asian (SAS) AF: 0.496 AC: 2373 AN: 4786

European-Finnish (FIN) AF: 0.400 AC: 4210 AN: 10524

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.452 AC: 30687 AN: 67954

Other (OTH) AF: 0.415 AC: 875 AN: 2106

Alfa AF: 0.454 Hom.: 29034

Bravo AF: 0.451

Asia WGS AF: 0.548 AC: 1902 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.48
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs6502198; hg19: chr17-12537978;