1-225449904-A-G

Position:

• chr1-225449904-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433058.1(LINC02765):​n.62-1319T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,066 control chromosomes in the GnomAD database, including 53,069 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 0.83 (53069 hom., cov: 31)
• Consequence: LINC02765 ENST00000433058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664

Genes affected

LINC02765 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02765	NR_187302.1	n.828-1319T>C		intron_variant
LINC02765	NR_187303.1	n.728-1319T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02765	ENST00000428642.1	n.122-2386T>C		intron_variant		3
LINC02765	ENST00000433058.1	n.62-1319T>C		intron_variant		2
LINC02765	ENST00000651771.1	n.425+575T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126463 AN: 151948 Hom.: 53035 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.832 AC: 126548 AN: 152066 Hom.: 53069 Cov.: 31 AF XY: 0.830 AC XY: 61681 AN XY: 74334

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.851

Alfa AF: 0.865 Hom.: 62253

Bravo AF: 0.833

Asia WGS AF: 0.764 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6426075; hg19: chr1-225637606;