ENST00000433079.5:n.361+49238T>C

Variant names:

• chr7-131057307-A-G
• rs7803075
• ENST00000433079.5:n.361+49238T>C

Variant summary

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

The ENST00000433079.5(LINC-PINT):​n.361+49238T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 19 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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.724 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC-PINT	NR_015431.2		n.1265-4752T>C		intron	N/A
	LINC-PINT	NR_024153.2		n.361+49238T>C		intron	N/A
	LINC-PINT	NR_109850.1		n.1265-4752T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC-PINT	ENST00000433079.5	TSL:1	n.361+49238T>C		intron	N/A
	LINC-PINT	ENST00000423414.5	TSL:4	n.344+50413T>C		intron	N/A
	LINC-PINT	ENST00000429901.3	TSL:4	n.425-4752T>C		intron	N/A

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

African (AFR) AF: 0.134 AC: 5583 AN: 41528

American (AMR) AF: 0.492 AC: 7523 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2332 AN: 3470

East Asian (EAS) AF: 0.123 AC: 636 AN: 5184

South Asian (SAS) AF: 0.415 AC: 2002 AN: 4824

European-Finnish (FIN) AF: 0.611 AC: 6458 AN: 10562

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.729 AC: 49593 AN: 67994

Other (OTH) AF: 0.534 AC: 1127 AN: 2112

Alfa AF: 0.620 Hom.: 60385

Bravo AF: 0.473

Asia WGS AF: 0.215 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.68
PhyloP100		-0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7803075;

hg19: chr7-130742066;