rs599250

chr1-95545165-T-Achr1-95545165-T-Cchr1-95545165-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02607	ENST00000456933.1	n.307+6473T>A		intron_variant, non_coding_transcript_variant		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;