rs4141794

Positions:

• chr7-130982499-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433079.5(LINC-PINT):​n.418+1554C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,050 control chromosomes in the GnomAD database, including 9,144 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 0.34 (9144 hom., cov: 32)
• Consequence: LINC-PINT ENST00000433079.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

LINC-PINT (HGNC:26885): (long intergenic non-protein coding RNA, p53 induced transcript) Predicted to act upstream of or within several processes, including adipose tissue development; adult somatic muscle development; and hair follicle development. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC-PINT	NR_015431.2	n.1452+1554C>T		intron_variant, non_coding_transcript_variant
LINC-PINT	NR_024153.2	n.418+1554C>T		intron_variant, non_coding_transcript_variant
LINC-PINT	NR_109850.1	n.1576+1554C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC-PINT	ENST00000642963.1	n.397+1554C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52116 AN: 151932 Hom.: 9132 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.343 AC: 52140 AN: 152050 Hom.: 9144 Cov.: 32 AF XY: 0.341 AC XY: 25330 AN XY: 74312

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.327

Alfa AF: 0.362 Hom.: 18241

Bravo AF: 0.348

Asia WGS AF: 0.326 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4141794; hg19: chr7-130667258;