rs599250

Variant names:

• chr1-95545165-T-A
• rs599250
• ENST00000456933.1:n.307+6473T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-95545165-T-A
• chr1-95545165-T-C
• chr1-95545165-T-G

Variant summary

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

The ENST00000456933.1(LINC02607):​n.307+6473T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 151,876 control chromosomes in the GnomAD database, including 62,603 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 0.91 (62603 hom., cov: 31)
• Consequence: LINC02607 ENST00000456933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 2 publications found

Genes affected

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

ENSG00000304521 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02607	ENST00000456933.1	TSL:3	n.307+6473T>A		intron	N/A
	ENSG00000304521	ENST00000804131.1		n.97-2581A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.907 AC: 137617 AN: 151758 Hom.: 62563 Cov.: 31

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.907 AC: 137709 AN: 151876 Hom.: 62603 Cov.: 31 AF XY: 0.903 AC XY: 67041 AN XY: 74236

African (AFR) AF: 0.937 AC: 38865 AN: 41480

American (AMR) AF: 0.817 AC: 12435 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 3231 AN: 3472

East Asian (EAS) AF: 0.813 AC: 4199 AN: 5162

South Asian (SAS) AF: 0.892 AC: 4303 AN: 4822

European-Finnish (FIN) AF: 0.919 AC: 9734 AN: 10590

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 61935 AN: 67818

Other (OTH) AF: 0.893 AC: 1882 AN: 2108

Alfa AF: 0.914 Hom.: 7889

Bravo AF: 0.902

Asia WGS AF: 0.813 AC: 2829 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.36
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs599250;

hg19: chr1-96010721;