chr7-130969092-C-A

Variant names:

• chr7-130969092-C-A
• rs2048672
• ENST00000433079.5:n.418+14961G>T

Variant summary

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

The ENST00000433079.5(LINC-PINT):​n.418+14961G>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 24 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433079.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC-PINT	NR_015431.2		n.1452+14961G>T		intron	N/A
	LINC-PINT	NR_024153.2		n.418+14961G>T		intron	N/A
	LINC-PINT	NR_109850.1		n.1576+14961G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC-PINT	ENST00000433079.5	TSL:1	n.418+14961G>T		intron	N/A
	LINC-PINT	ENST00000423414.5	TSL:4	n.401+14961G>T		intron	N/A
	LINC-PINT	ENST00000431189.3	TSL:3	n.613-1575G>T		intron	N/A

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

African (AFR) AF: 0.711 AC: 29485 AN: 41488

American (AMR) AF: 0.466 AC: 7113 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1039 AN: 3468

East Asian (EAS) AF: 0.571 AC: 2956 AN: 5174

South Asian (SAS) AF: 0.428 AC: 2061 AN: 4816

European-Finnish (FIN) AF: 0.429 AC: 4526 AN: 10548

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19857 AN: 67958

Other (OTH) AF: 0.406 AC: 857 AN: 2110

Alfa AF: 0.362 Hom.: 17611

Bravo AF: 0.459

Asia WGS AF: 0.510 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.40
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2048672; hg19: chr7-130653851;