rs7803075

chr7-131057307-A-G

Variant summary

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

The ENST00000433079.5(LINC-PINT):n.361+49238T>C 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 0.5 in 152,160 control chromosomes in the GnomAD database, including 24,326 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 0.50 (24326 hom., cov: 33)
• Consequence: LINC-PINT ENST00000433079.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC-PINT	NR_015431.2	n.1265-4752T>C		intron_variant, non_coding_transcript_variant
LINC-PINT	NR_024153.2	n.361+49238T>C		intron_variant, non_coding_transcript_variant
LINC-PINT	NR_109850.1	n.1265-4752T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC-PINT	ENST00000642963.1	n.210-4752T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76109 AN: 152044 Hom.: 24338 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.500 AC: 76081 AN: 152160 Hom.: 24326 Cov.: 33 AF XY: 0.491 AC XY: 36520 AN XY: 74386

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.534

Alfa AF: 0.671 Hom.: 39645

Bravo AF: 0.473

Asia WGS AF: 0.215 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	14
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7803075; hg19: chr7-130742066;