rs1658957

Variant names:

• chr9-6672097-A-G
• rs1658957
• ENST00000813381.1:n.882A>G

Variant summary

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

The ENST00000813381.1(LINC02851):​n.882A>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 0.519 in 152,000 control chromosomes in the GnomAD database, including 20,922 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 0.52 (20922 hom., cov: 33)
• Consequence: LINC02851 ENST00000813381.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 5 publications found

Genes affected

LINC02851 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 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
LINC02851	ENST00000813381.1	n.882A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02851	ENST00000687289.2	n.441+2369A>G		intron_variant	Intron 2 of 2
LINC02851	ENST00000813368.1	n.409+2369A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78823 AN: 151882 Hom.: 20891 Cov.: 33

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.519 AC: 78894 AN: 152000 Hom.: 20922 Cov.: 33 AF XY: 0.514 AC XY: 38155 AN XY: 74292

African (AFR) AF: 0.632 AC: 26193 AN: 41462

American (AMR) AF: 0.518 AC: 7897 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1824 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1439 AN: 5154

South Asian (SAS) AF: 0.423 AC: 2041 AN: 4830

European-Finnish (FIN) AF: 0.430 AC: 4540 AN: 10552

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33172 AN: 67972

Other (OTH) AF: 0.534 AC: 1125 AN: 2108

Alfa AF: 0.495 Hom.: 16796

Bravo AF: 0.527

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.62
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1658957; hg19: chr9-6672097;