rs1795030

Variant names:

• chr1-214124300-A-G
• rs1795030
• ENST00000637598.1:n.662-51862T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-214124300-A-G
• chr1-214124300-A-T

Variant summary

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

The ENST00000637598.1(LINC02775):​n.662-51862T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,038 control chromosomes in the GnomAD database, including 22,684 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 0.53 (22684 hom., cov: 31)
• Consequence: LINC02775 ENST00000637598.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 1 publications found

Genes affected

LINC02775 (HGNC:54294): (long intergenic non-protein coding RNA 2775)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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
LINC02775	ENST00000637598.1	n.662-51862T>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79963 AN: 151918 Hom.: 22649 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.527 AC: 80051 AN: 152038 Hom.: 22684 Cov.: 31 AF XY: 0.539 AC XY: 40062 AN XY: 74316

African (AFR) AF: 0.633 AC: 26267 AN: 41480

American (AMR) AF: 0.598 AC: 9131 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1207 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5143 AN: 5174

South Asian (SAS) AF: 0.700 AC: 3366 AN: 4810

European-Finnish (FIN) AF: 0.500 AC: 5285 AN: 10564

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.414 AC: 28096 AN: 67946

Other (OTH) AF: 0.497 AC: 1048 AN: 2108

Alfa AF: 0.445 Hom.: 19968

Bravo AF: 0.535

Asia WGS AF: 0.840 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.82
DANN	Benign	0.44
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs1795030; hg19: chr1-214297643;