ENST00000648995.2:n.325+32585C>T

Variant names:

• chr10-6770213-C-T
• rs1822279
• ENST00000648995.2:n.325+32585C>T

Variant summary

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

The ENST00000648995.2(LINP1):​n.325+32585C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.064 in 152,244 control chromosomes in the GnomAD database, including 906 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 (906 hom., cov: 32)
• Consequence: LINP1 ENST00000648995.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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	ENST00000648995.2	n.325+32585C>T		intron_variant	Intron 1 of 3
LINP1	ENST00000650342.1	n.375-11091C>T		intron_variant	Intron 3 of 6
LINP1	ENST00000829822.1	n.257-11091C>T		intron_variant	Intron 1 of 4
LINP1	ENST00000829823.1	n.255+32585C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0639 AC: 9725 AN: 152126 Hom.: 902 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.00842

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0640 AC: 9745 AN: 152244 Hom.: 906 Cov.: 32 AF XY: 0.0630 AC XY: 4693 AN XY: 74448

African (AFR) AF: 0.203 AC: 8415 AN: 41500

American (AMR) AF: 0.0274 AC: 419 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.0172 AC: 83 AN: 4820

European-Finnish (FIN) AF: 0.00245 AC: 26 AN: 10628

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.00842 AC: 573 AN: 68026

Other (OTH) AF: 0.0516 AC: 109 AN: 2114

Alfa AF: 0.0406 Hom.: 58

Bravo AF: 0.0717

Asia WGS AF: 0.0160 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.76
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1822279; hg19: chr10-6812175;