chr1-207955720-A-G

Variant names:

• chr1-207955720-A-G
• rs11578508
• ENST00000742950.1:n.311A>G

Variant summary

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

The ENST00000742950.1(LINC02767):​n.311A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,148 control chromosomes in the GnomAD database, including 6,668 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 0.29 (6668 hom., cov: 33)
• Consequence: LINC02767 ENST00000742950.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74
• Publications: 15 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 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	ENST00000742950.1	n.311A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02767	ENST00000742961.1	n.218A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02767	ENST00000742948.1	n.242-4395A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43408 AN: 152030 Hom.: 6666 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.285 AC: 43422 AN: 152148 Hom.: 6668 Cov.: 33 AF XY: 0.276 AC XY: 20520 AN XY: 74396

African (AFR) AF: 0.230 AC: 9560 AN: 41500

American (AMR) AF: 0.254 AC: 3884 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3472

East Asian (EAS) AF: 0.0390 AC: 202 AN: 5184

South Asian (SAS) AF: 0.169 AC: 812 AN: 4816

European-Finnish (FIN) AF: 0.266 AC: 2820 AN: 10588

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23874 AN: 67992

Other (OTH) AF: 0.288 AC: 608 AN: 2112

Alfa AF: 0.318 Hom.: 11845

Bravo AF: 0.285

Asia WGS AF: 0.113 AC: 395 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	0.038
DANN	Benign	0.16
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs11578508; hg19: chr1-208129065;