chr7-130976069-C-G

Variant names:

• chr7-130976069-C-G
• rs205737
• ENST00000433079.5:n.418+7984G>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.418+7984G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 152,028 control chromosomes in the GnomAD database, including 28,081 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 0.61 (28081 hom., cov: 31)
• Consequence: LINC-PINT ENST00000433079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 4 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 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.1452+7984G>C		intron	N/A
	LINC-PINT	NR_024153.2		n.418+7984G>C		intron	N/A
	LINC-PINT	NR_109850.1		n.1576+7984G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC-PINT	ENST00000433079.5	TSL:1	n.418+7984G>C		intron	N/A
	LINC-PINT	ENST00000423414.5	TSL:4	n.401+7984G>C		intron	N/A
	LINC-PINT	ENST00000431189.3	TSL:3	n.612+7984G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91958 AN: 151910 Hom.: 28051 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.605 AC: 92033 AN: 152028 Hom.: 28081 Cov.: 31 AF XY: 0.606 AC XY: 45000 AN XY: 74292

African (AFR) AF: 0.560 AC: 23226 AN: 41444

American (AMR) AF: 0.558 AC: 8520 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2603 AN: 3472

East Asian (EAS) AF: 0.696 AC: 3600 AN: 5174

South Asian (SAS) AF: 0.598 AC: 2882 AN: 4822

European-Finnish (FIN) AF: 0.647 AC: 6833 AN: 10556

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42194 AN: 67972

Other (OTH) AF: 0.636 AC: 1343 AN: 2112

Alfa AF: 0.607 Hom.: 3368

Bravo AF: 0.599

Asia WGS AF: 0.643 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.34
DANN	Benign	0.24
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs205737; hg19: chr7-130660828;