chr10-6794725-C-T

Variant names:

• chr10-6794725-C-T
• rs2387742
• ENST00000436383.3:n.538+13239C>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+13239C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0635 in 152,048 control chromosomes in the GnomAD database, including 567 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 0.064 (567 hom., cov: 31)
• Consequence: LINP1 ENST00000436383.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436383.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00707	NR_038291.1		n.473+13239C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINP1	ENST00000436383.3	TSL:2	n.538+13239C>T		intron	N/A
	LINP1	ENST00000648093.1		n.522+13239C>T		intron	N/A
	LINP1	ENST00000648398.1		n.483+13239C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9662 AN: 151930 Hom.: 568 Cov.: 31

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0154

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0726

Gnomad OTH AF: 0.0738

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

GnomAD4 genome AF: 0.0635 AC: 9657 AN: 152048 Hom.: 567 Cov.: 31 AF XY: 0.0635 AC XY: 4717 AN XY: 74340

African (AFR) AF: 0.0165 AC: 685 AN: 41494

American (AMR) AF: 0.0813 AC: 1241 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3468

East Asian (EAS) AF: 0.298 AC: 1523 AN: 5108

South Asian (SAS) AF: 0.156 AC: 749 AN: 4814

European-Finnish (FIN) AF: 0.0154 AC: 163 AN: 10580

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0726 AC: 4936 AN: 68002

Other (OTH) AF: 0.0726 AC: 153 AN: 2108

Alfa AF: 0.0730 Hom.: 233

Bravo AF: 0.0657

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.75
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs2387742; hg19: chr10-6836687;