rs643930

Variant names:

• chr1-207984996-G-A
• rs643930
• ENST00000742951.1:n.458-630G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-207984996-G-A
• chr1-207984996-G-C
• chr1-207984996-G-T

Variant summary

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

The ENST00000742951.1(LINC02767):​n.458-630G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,082 control chromosomes in the GnomAD database, including 27,251 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 0.59 (27251 hom., cov: 33)
• Consequence: LINC02767 ENST00000742951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 3 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000742951.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02767	ENST00000742951.1		n.458-630G>A		intron	N/A
	LINC02767	ENST00000742952.1		n.467-630G>A		intron	N/A
	LINC02767	ENST00000742953.1		n.296-1551G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90099 AN: 151964 Hom.: 27224 Cov.: 33

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.593 AC: 90165 AN: 152082 Hom.: 27251 Cov.: 33 AF XY: 0.603 AC XY: 44822 AN XY: 74348

African (AFR) AF: 0.497 AC: 20615 AN: 41468

American (AMR) AF: 0.579 AC: 8844 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2439 AN: 3470

East Asian (EAS) AF: 0.818 AC: 4243 AN: 5186

South Asian (SAS) AF: 0.684 AC: 3298 AN: 4824

European-Finnish (FIN) AF: 0.723 AC: 7649 AN: 10578

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41286 AN: 67964

Other (OTH) AF: 0.585 AC: 1234 AN: 2110

Alfa AF: 0.616 Hom.: 25650

Bravo AF: 0.578

Asia WGS AF: 0.668 AC: 2321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs643930;

hg19: chr1-208158341;