rs11254492

Variant names:

• chr10-6763524-G-A
• rs11254492
• ENST00000648995.2:n.325+25896G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-6763524-G-A
• chr10-6763524-G-C

Variant summary

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

The ENST00000648995.2(LINP1):​n.325+25896G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0386 in 152,250 control chromosomes in the GnomAD database, including 162 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 0.039 (162 hom., cov: 32)
• Consequence: LINP1 ENST00000648995.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0598 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+25896G>A		intron_variant	Intron 1 of 3
LINP1	ENST00000650342.1	n.375-17780G>A		intron_variant	Intron 3 of 6
LINP1	ENST00000829822.1	n.257-17780G>A		intron_variant	Intron 1 of 4
LINP1	ENST00000829823.1	n.255+25896G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0387 AC: 5880 AN: 152132 Hom.: 161 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.0183

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0386 AC: 5878 AN: 152250 Hom.: 162 Cov.: 32 AF XY: 0.0356 AC XY: 2647 AN XY: 74434

African (AFR) AF: 0.0103 AC: 426 AN: 41560

American (AMR) AF: 0.0415 AC: 635 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4828

European-Finnish (FIN) AF: 0.0183 AC: 194 AN: 10594

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0614 AC: 4176 AN: 68010

Other (OTH) AF: 0.0469 AC: 99 AN: 2110

Alfa AF: 0.0545 Hom.: 402

Bravo AF: 0.0385

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.62
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs11254492; hg19: chr10-6805486;