rs2439903

Variant names:

• chr10-6789898-G-A
• rs2439903
• ENST00000649110.1:n.1019G>A

Variant summary

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

The ENST00000649110.1(LINP1):​n.1019G>A 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 0.093 in 152,104 control chromosomes in the GnomAD database, including 1,125 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 0.093 (1125 hom., cov: 31)
• Consequence: LINP1 ENST00000649110.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 2 publications found

Genes affected

LINP1 (HGNC:53170): (lncRNA in non-homologous end joining pathway 1)

LINC00707 (HGNC:44691): (long intergenic non-protein coding RNA 707)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00707	NR_038291.1	n.473+8412G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINP1	ENST00000649110.1	n.1019G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LINP1	ENST00000436383.3	n.538+8412G>A		intron_variant	Intron 2 of 4	2
LINP1	ENST00000648093.1	n.522+8412G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.0929 AC: 14121 AN: 151986 Hom.: 1119 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0930 AC: 14140 AN: 152104 Hom.: 1125 Cov.: 31 AF XY: 0.0936 AC XY: 6960 AN XY: 74356

African (AFR) AF: 0.217 AC: 8982 AN: 41444

American (AMR) AF: 0.0697 AC: 1064 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0807 AC: 280 AN: 3470

East Asian (EAS) AF: 0.0940 AC: 487 AN: 5182

South Asian (SAS) AF: 0.104 AC: 501 AN: 4810

European-Finnish (FIN) AF: 0.0333 AC: 353 AN: 10610

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0336 AC: 2283 AN: 68000

Other (OTH) AF: 0.0767 AC: 162 AN: 2112

Alfa AF: 0.0531 Hom.: 1708

Bravo AF: 0.101

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.0
DANN	Benign	0.28
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2439903; hg19: chr10-6831860;