rs2745967

Variant names:

• chr1-207955377-G-A
• rs2745967
• ENST00000742948.1:n.242-4738G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-207955377-G-A
• chr1-207955377-G-C

Variant summary

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

The ENST00000742948.1(LINC02767):​n.242-4738G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,098 control chromosomes in the GnomAD database, including 29,215 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 0.61 (29215 hom., cov: 33)
• Consequence: LINC02767 ENST00000742948.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 24 publications found

Genes affected

LINC02767 (HGNC:54287): (long intergenic non-protein coding RNA 2767)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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
LINC02767	ENST00000742948.1	n.242-4738G>A		intron_variant	Intron 2 of 3
LINC02767	ENST00000742949.1	n.249-4738G>A		intron_variant	Intron 2 of 3
LINC02767	ENST00000742950.1	n.226-258G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92297 AN: 151982 Hom.: 29193 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.607 AC: 92359 AN: 152098 Hom.: 29215 Cov.: 33 AF XY: 0.619 AC XY: 46055 AN XY: 74354

African (AFR) AF: 0.447 AC: 18545 AN: 41478

American (AMR) AF: 0.681 AC: 10395 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2391 AN: 3470

East Asian (EAS) AF: 0.940 AC: 4872 AN: 5182

South Asian (SAS) AF: 0.796 AC: 3838 AN: 4824

European-Finnish (FIN) AF: 0.728 AC: 7710 AN: 10596

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42946 AN: 67976

Other (OTH) AF: 0.609 AC: 1283 AN: 2106

Alfa AF: 0.634 Hom.: 73022

Bravo AF: 0.595

Asia WGS AF: 0.814 AC: 2828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.43
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2745967; hg19: chr1-208128722;