ENST00000456933.1:n.307+85483G>A

Variant names:

• chr1-95624175-G-A
• rs1858111
• ENST00000456933.1:n.307+85483G>A

Variant summary

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

The ENST00000456933.1(LINC02607):​n.307+85483G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,002 control chromosomes in the GnomAD database, including 16,969 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 0.46 (16969 hom., cov: 32)
• Consequence: LINC02607 ENST00000456933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 4 publications found

Genes affected

LINC02607 (HGNC:54049): (long intergenic non-protein coding RNA 2607)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456933.1. 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
	LINC02607	ENST00000456933.1	TSL:3	n.307+85483G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70383 AN: 151884 Hom.: 16946 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.464 AC: 70463 AN: 152002 Hom.: 16969 Cov.: 32 AF XY: 0.470 AC XY: 34915 AN XY: 74290

African (AFR) AF: 0.467 AC: 19359 AN: 41466

American (AMR) AF: 0.540 AC: 8243 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1719 AN: 3468

East Asian (EAS) AF: 0.853 AC: 4405 AN: 5164

South Asian (SAS) AF: 0.572 AC: 2757 AN: 4818

European-Finnish (FIN) AF: 0.385 AC: 4066 AN: 10552

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28372 AN: 67944

Other (OTH) AF: 0.485 AC: 1025 AN: 2114

Alfa AF: 0.436 Hom.: 26117

Bravo AF: 0.475

Asia WGS AF: 0.708 AC: 2458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.43
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1858111; hg19: chr1-96089731;