1-207955510-G-A

Variant names:

• chr1-207955510-G-A
• rs11579848
• ENST00000742948.1:n.242-4605G>A

Variant summary

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

The ENST00000742948.1(LINC02767):​n.242-4605G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,162 control chromosomes in the GnomAD database, including 6,328 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 0.28 (6328 hom., cov: 33)
• Consequence: LINC02767 ENST00000742948.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.819
• Publications: 7 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=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000742948.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02767	ENST00000742948.1		n.242-4605G>A		intron	N/A
	LINC02767	ENST00000742949.1		n.249-4605G>A		intron	N/A
	LINC02767	ENST00000742950.1		n.226-125G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41991 AN: 152044 Hom.: 6326 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.276 AC: 41995 AN: 152162 Hom.: 6328 Cov.: 33 AF XY: 0.266 AC XY: 19803 AN XY: 74394

African (AFR) AF: 0.203 AC: 8428 AN: 41522

American (AMR) AF: 0.247 AC: 3782 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3470

East Asian (EAS) AF: 0.0386 AC: 200 AN: 5182

South Asian (SAS) AF: 0.169 AC: 814 AN: 4826

European-Finnish (FIN) AF: 0.261 AC: 2759 AN: 10566

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23833 AN: 67996

Other (OTH) AF: 0.281 AC: 594 AN: 2112

Alfa AF: 0.322 Hom.: 31735

Bravo AF: 0.274

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.77
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs11579848; hg19: chr1-208128855;