ENST00000648995.2:n.325+9873C>T

Variant names:

• chr10-6747501-C-T
• rs12570744
• ENST00000648995.2:n.325+9873C>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+9873C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,082 control chromosomes in the GnomAD database, including 3,683 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 0.21 (3683 hom., cov: 32)
• Consequence: LINP1 ENST00000648995.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 4 publications found

Genes affected

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

ENSG00000307985 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648995.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINP1	ENST00000648995.2		n.325+9873C>T		intron	N/A
	LINP1	ENST00000650342.1		n.375-33803C>T		intron	N/A
	LINP1	ENST00000829822.1		n.256+9873C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31435 AN: 151964 Hom.: 3673 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.207 AC: 31481 AN: 152082 Hom.: 3683 Cov.: 32 AF XY: 0.211 AC XY: 15686 AN XY: 74338

African (AFR) AF: 0.203 AC: 8399 AN: 41468

American (AMR) AF: 0.263 AC: 4015 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3466

East Asian (EAS) AF: 0.543 AC: 2805 AN: 5164

South Asian (SAS) AF: 0.299 AC: 1437 AN: 4806

European-Finnish (FIN) AF: 0.131 AC: 1385 AN: 10598

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11945 AN: 68000

Other (OTH) AF: 0.204 AC: 429 AN: 2108

Alfa AF: 0.196 Hom.: 10348

Bravo AF: 0.218

Asia WGS AF: 0.414 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.60
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs12570744; hg19: chr10-6789463;