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. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02607	ENST00000456933.1	n.307+6473T>A		intron_variant	Intron 2 of 3	3

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

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.931

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.892

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.893

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs599250; hg19: chr1-96010721;