rs11254686

Variant names:

• chr10-6796980-C-T
• rs11254686
• ENST00000436383.3:n.538+15494C>T

Variant summary

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

The ENST00000436383.3(LINP1):​n.538+15494C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0926 in 152,170 control chromosomes in the GnomAD database, including 821 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 (821 hom., cov: 31)
• Consequence: LINP1 ENST00000436383.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 3 publications found

Genes affected

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

ENSG00000307964 (HGNC:):

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00707	NR_038291.1	n.473+15494C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINP1	ENST00000436383.3	n.538+15494C>T		intron_variant	Intron 2 of 4	2
LINP1	ENST00000648093.1	n.523-13619C>T		intron_variant	Intron 2 of 6
LINP1	ENST00000648398.1	n.484-15270C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 14064 AN: 152052 Hom.: 817 Cov.: 31

Gnomad AFR AF: 0.0466

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.0758

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0745

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0926 AC: 14084 AN: 152170 Hom.: 821 Cov.: 31 AF XY: 0.0940 AC XY: 6990 AN XY: 74380

African (AFR) AF: 0.0469 AC: 1946 AN: 41522

American (AMR) AF: 0.0756 AC: 1156 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 713 AN: 3470

East Asian (EAS) AF: 0.217 AC: 1122 AN: 5170

South Asian (SAS) AF: 0.205 AC: 991 AN: 4824

European-Finnish (FIN) AF: 0.0745 AC: 789 AN: 10586

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6823 AN: 67994

Other (OTH) AF: 0.117 AC: 246 AN: 2110

Alfa AF: 0.0888 Hom.: 115

Bravo AF: 0.0900

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.69
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs11254686; hg19: chr10-6838942;