rs1327235

Variant names:

• chr20-10988382-A-G
• rs1327235
• ENST00000378252.3:n.290+209A>G

Variant summary

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

The ENST00000378252.3(LINC02871):​n.290+209A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,944 control chromosomes in the GnomAD database, including 16,408 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 0.46 (16408 hom., cov: 32)
• Consequence: LINC02871 ENST00000378252.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 70 publications found

Genes affected

LINC02871 (HGNC:16180): (long intergenic non-protein coding RNA 2871)

ENSG00000270792 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 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
LINC02871	ENST00000378252.3	n.290+209A>G		intron_variant	Intron 3 of 10	2
LINC02871	ENST00000603180.6	n.231+209A>G		intron_variant	Intron 3 of 8	4
LINC02871	ENST00000603985.1	n.83+1625A>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69991 AN: 151826 Hom.: 16395 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.461 AC: 70038 AN: 151944 Hom.: 16408 Cov.: 32 AF XY: 0.457 AC XY: 33918 AN XY: 74272

African (AFR) AF: 0.506 AC: 20974 AN: 41430

American (AMR) AF: 0.324 AC: 4945 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3470

East Asian (EAS) AF: 0.546 AC: 2816 AN: 5158

South Asian (SAS) AF: 0.475 AC: 2287 AN: 4812

European-Finnish (FIN) AF: 0.427 AC: 4496 AN: 10536

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31706 AN: 67960

Other (OTH) AF: 0.451 AC: 950 AN: 2108

Alfa AF: 0.463 Hom.: 51057

Bravo AF: 0.452

Asia WGS AF: 0.500 AC: 1737 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.062
DANN	Benign	0.45
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1327235; hg19: chr20-10969030;