ENST00000577679.1:n.406-6335G>T

Variant names:

• chr17-12628666-G-T
• rs1401539
• ENST00000577679.1:n.406-6335G>T

Variant summary

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

The ENST00000577679.1(LINC00670):​n.406-6335G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,062 control chromosomes in the GnomAD database, including 2,218 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 0.15 (2218 hom., cov: 33)
• Consequence: LINC00670 ENST00000577679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521
• Publications: 4 publications found

Genes affected

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

ENSG00000287462 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00670	NR_034144.1	n.419-6335G>T		intron_variant	Intron 2 of 2
LINC00670	NR_034145.1	n.581-6335G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00670	ENST00000577679.1	n.406-6335G>T		intron_variant	Intron 2 of 2	1
LINC00670	ENST00000313495.7	n.767-6335G>T		intron_variant	Intron 3 of 3	2
LINC00670	ENST00000577863.2	n.608-6335G>T		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23439 AN: 151944 Hom.: 2219 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0973

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.154 AC: 23457 AN: 152062 Hom.: 2218 Cov.: 33 AF XY: 0.165 AC XY: 12295 AN XY: 74336

African (AFR) AF: 0.165 AC: 6847 AN: 41480

American (AMR) AF: 0.235 AC: 3593 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 421 AN: 3470

East Asian (EAS) AF: 0.398 AC: 2054 AN: 5156

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4814

European-Finnish (FIN) AF: 0.249 AC: 2634 AN: 10578

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0973 AC: 6614 AN: 67982

Other (OTH) AF: 0.122 AC: 257 AN: 2108

Alfa AF: 0.123 Hom.: 3409

Bravo AF: 0.154

Asia WGS AF: 0.269 AC: 936 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	2.7
DANN	Benign	0.36
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs1401539; hg19: chr17-12531983;