17-12634661-T-C

Position:

• chr17-12634661-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_034145.1(LINC00670):​n.581-340T>C variant causes a intron, non coding transcript 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 NR_034145.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00670	NR_034145.1	n.581-340T>C		intron_variant, non_coding_transcript_variant
LINC00670	NR_034144.1	n.419-340T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00670	ENST00000577863.2	n.608-340T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.415

Alfa AF: 0.448 Hom.: 7214

Bravo AF: 0.451

Asia WGS AF: 0.548 AC: 1902 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6502198; hg19: chr17-12537978;