rs2048672

chr7-130969092-C-Achr7-130969092-C-G

Variant summary

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

The ENST00000433079.5(LINC-PINT):n.418+14961G>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 0.448 in 152,042 control chromosomes in the GnomAD database, including 17,761 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 0.45 (17761 hom., cov: 32)
• Consequence: LINC-PINT ENST00000433079.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC-PINT	NR_015431.2	n.1452+14961G>T		intron_variant, non_coding_transcript_variant
LINC-PINT	NR_024153.2	n.418+14961G>T		intron_variant, non_coding_transcript_variant
LINC-PINT	NR_109850.1	n.1576+14961G>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+14961G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68027 AN: 151924 Hom.: 17711 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.448 AC: 68148 AN: 152042 Hom.: 17761 Cov.: 32 AF XY: 0.455 AC XY: 33816 AN XY: 74312

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.406

Alfa AF: 0.320 Hom.: 4703

Bravo AF: 0.459

Asia WGS AF: 0.510 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.27
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2048672; hg19: chr7-130653851;