chr10-6689494-C-G

Variant names:

• chr10-6689494-C-G
• rs10508311
• ENST00000650342.1:n.229+6444C>G

Variant summary

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

The ENST00000650342.1(LINP1):​n.229+6444C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,194 control chromosomes in the GnomAD database, including 1,858 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 0.14 (1858 hom., cov: 32)
• Consequence: LINP1 ENST00000650342.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.175 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
LINP1	ENST00000650342.1	n.229+6444C>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21513 AN: 152076 Hom.: 1855 Cov.: 32

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.141 AC: 21509 AN: 152194 Hom.: 1858 Cov.: 32 AF XY: 0.146 AC XY: 10848 AN XY: 74420

African (AFR) AF: 0.0531 AC: 2205 AN: 41542

American (AMR) AF: 0.140 AC: 2141 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3472

East Asian (EAS) AF: 0.153 AC: 790 AN: 5168

South Asian (SAS) AF: 0.152 AC: 734 AN: 4822

European-Finnish (FIN) AF: 0.265 AC: 2809 AN: 10586

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12095 AN: 67992

Other (OTH) AF: 0.144 AC: 304 AN: 2116

Alfa AF: 0.164 Hom.: 290

Bravo AF: 0.127

Asia WGS AF: 0.118 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.3
DANN	Benign	0.52
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs10508311; hg19: chr10-6731456;