7-130899925-C-G

Variant names:

• chr7-130899925-C-G
• rs125124
• ENST00000418546.1:n.290+12185G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000418546.1(LINC-PINT):​n.290+12185G>C variant causes a intron 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 ENST00000418546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC-PINT	NR_034120.1	n.403+12185G>C		intron_variant	Intron 2 of 3
LINC-PINT	NR_110472.1	n.403+12185G>C		intron_variant	Intron 2 of 3
LINC-PINT	NR_110473.1	n.403+12185G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC-PINT	ENST00000418546.1	n.290+12185G>C		intron_variant	Intron 2 of 2	4
LINC-PINT	ENST00000432045.6	n.403+12185G>C		intron_variant	Intron 2 of 3	2
LINC-PINT	ENST00000447307.5	n.269+12185G>C		intron_variant	Intron 2 of 3	3

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

African (AFR) AF: 0.198 AC: 8201 AN: 41492

American (AMR) AF: 0.309 AC: 4714 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 894 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2219 AN: 5166

South Asian (SAS) AF: 0.329 AC: 1586 AN: 4826

European-Finnish (FIN) AF: 0.372 AC: 3945 AN: 10594

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20113 AN: 67988

Other (OTH) AF: 0.304 AC: 641 AN: 2112

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs125124; hg19: chr7-130584684;