3-128568900-G-T

Variant names:

• chr3-128568900-G-T
• rs2712421
• ENST00000753242.1:n.75-3158C>A

Variant summary

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

The ENST00000753242.1(LINC01565):​n.75-3158C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,198 control chromosomes in the GnomAD database, including 38,702 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 0.71 (38702 hom., cov: 34)
• Consequence: LINC01565 ENST00000753242.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 2 publications found

Genes affected

LINC01565 (HGNC:17099): (long intergenic non-protein coding RNA 1565)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753242.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01565	ENST00000753242.1		n.75-3158C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107850 AN: 152080 Hom.: 38645 Cov.: 34

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.709 AC: 107963 AN: 152198 Hom.: 38702 Cov.: 34 AF XY: 0.716 AC XY: 53317 AN XY: 74420

African (AFR) AF: 0.720 AC: 29897 AN: 41526

American (AMR) AF: 0.785 AC: 12012 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2536 AN: 3472

East Asian (EAS) AF: 0.973 AC: 5047 AN: 5186

South Asian (SAS) AF: 0.776 AC: 3745 AN: 4824

European-Finnish (FIN) AF: 0.700 AC: 7421 AN: 10602

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.662 AC: 45002 AN: 67976

Other (OTH) AF: 0.713 AC: 1508 AN: 2114

Alfa AF: 0.682 Hom.: 59147

Bravo AF: 0.716

Asia WGS AF: 0.872 AC: 3032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2712421; hg19: chr3-128287743;