chr9-6650885-G-A

Variant names:

• chr9-6650885-G-A
• rs2988418
• ENST00000413145.4:n.278+4800G>A

Variant summary

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

The ENST00000413145.4(LINC02851):​n.278+4800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,978 control chromosomes in the GnomAD database, including 12,453 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 0.35 (12453 hom., cov: 31)
• Consequence: LINC02851 ENST00000413145.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 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	ENST00000413145.4	n.278+4800G>A		intron_variant	Intron 1 of 2	2
LINC02851	ENST00000687289.2	n.256+4800G>A		intron_variant	Intron 1 of 2
LINC02851	ENST00000688297.3	n.277+4800G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53426 AN: 151860 Hom.: 12417 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.352 AC: 53526 AN: 151978 Hom.: 12453 Cov.: 31 AF XY: 0.357 AC XY: 26516 AN XY: 74292

African (AFR) AF: 0.620 AC: 25669 AN: 41428

American (AMR) AF: 0.377 AC: 5752 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3468

East Asian (EAS) AF: 0.709 AC: 3663 AN: 5164

South Asian (SAS) AF: 0.364 AC: 1758 AN: 4828

European-Finnish (FIN) AF: 0.257 AC: 2713 AN: 10562

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12522 AN: 67968

Other (OTH) AF: 0.320 AC: 674 AN: 2108

Alfa AF: 0.244 Hom.: 18810

Bravo AF: 0.375

Asia WGS AF: 0.542 AC: 1881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.56
DANN	Benign	0.79
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2988418; hg19: chr9-6650885;