7-130900794-T-G

Variant names:

• chr7-130900794-T-G
• rs157935
• ENST00000845347.1:n.703A>C

Variant summary

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

The ENST00000845347.1(LINC-PINT):​n.703A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,082 control chromosomes in the GnomAD database, including 6,649 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 0.29 (6649 hom., cov: 32)
• Consequence: LINC-PINT ENST00000845347.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 34 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000845347.1. 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_034120.1		n.403+11316A>C		intron	N/A
	LINC-PINT	NR_110472.1		n.403+11316A>C		intron	N/A
	LINC-PINT	NR_110473.1		n.403+11316A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC-PINT	ENST00000845347.1		n.703A>C		non_coding_transcript_exon	Exon 3 of 3
	LINC-PINT	ENST00000418546.1	TSL:4	n.290+11316A>C		intron	N/A
	LINC-PINT	ENST00000432045.6	TSL:2	n.403+11316A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43515 AN: 151964 Hom.: 6646 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.286 AC: 43535 AN: 152082 Hom.: 6649 Cov.: 32 AF XY: 0.294 AC XY: 21846 AN XY: 74352

African (AFR) AF: 0.204 AC: 8467 AN: 41498

American (AMR) AF: 0.310 AC: 4741 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3470

East Asian (EAS) AF: 0.441 AC: 2275 AN: 5162

South Asian (SAS) AF: 0.336 AC: 1621 AN: 4824

European-Finnish (FIN) AF: 0.411 AC: 4350 AN: 10584

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20159 AN: 67952

Other (OTH) AF: 0.308 AC: 650 AN: 2112

Alfa AF: 0.289 Hom.: 24916

Bravo AF: 0.273

Asia WGS AF: 0.386 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.58
DANN	Benign	0.59
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs157935; hg19: chr7-130585553;