rs2293748

Positions:

• chr7-130944734-T-C

Variant summary

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

The ENST00000642963.1(LINC-PINT):​n.513+986A>G 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 0.484 in 152,062 control chromosomes in the GnomAD database, including 18,446 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 0.48 (18446 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC-PINT ENST00000642963.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC-PINT	NR_015431.2	n.2554A>G		non_coding_transcript_exon_variant	5/5
LINC-PINT	NR_024153.2	n.690A>G		non_coding_transcript_exon_variant	5/5
LINC-PINT	NR_109850.1	n.2678A>G		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC-PINT	ENST00000642963.1	n.513+986A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73576 AN: 151944 Hom.: 18417 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.448

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.484 AC: 73664 AN: 152062 Hom.: 18446 Cov.: 32 AF XY: 0.489 AC XY: 36382 AN XY: 74336

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.448

Alfa AF: 0.511 Hom.: 27782

Bravo AF: 0.459

Asia WGS AF: 0.534 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2293748; hg19: chr7-130629493;