rs125124

chr7-130899925-C-Gchr7-130899925-C-T

Variant summary

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

The NR_110473.1(LINC-PINT):n.403+12185G>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 0.281 in 152,130 control chromosomes in the GnomAD database, including 6,356 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 0.28 (6356 hom., cov: 32)
• Consequence: LINC-PINT NR_110473.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

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]

LINC00513 (HGNC:43566): (long intergenic non-protein coding RNA 513)

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 (EAS) 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_110473.1	n.403+12185G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC-PINT	ENST00000642963.1	n.514-15529G>C		intron_variant, non_coding_transcript_variant
LINC00513	ENST00000653887.1	n.145-15037C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42662 AN: 152012 Hom.: 6352 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.281 AC: 42686 AN: 152130 Hom.: 6356 Cov.: 32 AF XY: 0.287 AC XY: 21313 AN XY: 74366

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.304

Alfa AF: 0.290 Hom.: 828

Bravo AF: 0.270

Asia WGS AF: 0.373 AC: 1295 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	0.67
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs125124; hg19: chr7-130584684;