7-131106894-G-A

Position:

• chr7-131106894-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000433079.5(LINC-PINT):​n.137C>T 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 0.109 in 152,188 control chromosomes in the GnomAD database, including 1,202 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.11 (1201 hom., cov: 31)
  • Exomes 𝑓: 0.089 (1 hom.)
• Consequence: LINC-PINT ENST00000433079.5 non_coding_transcript_exon
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -1.27

Genes affected

LINC-PINT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 7-131106894-G-A is Benign according to our data. Variant chr7-131106894-G-A is described in ClinVar as [Benign]. Clinvar id is 3059947.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC-PINT	NR_024153.2	n.137C>T		non_coding_transcript_exon_variant	1/5
LINC-PINT	NR_015431.2	n.1264+826C>T		intron_variant
LINC-PINT	NR_109850.1	n.1264+826C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC-PINT	ENST00000433079.5	n.137C>T		non_coding_transcript_exon_variant	1/5	1
LINC-PINT	ENST00000644804.1	n.142C>T		non_coding_transcript_exon_variant	1/4
LINC-PINT	ENST00000700935.1	n.142C>T		non_coding_transcript_exon_variant	1/5

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16535 AN: 151902 Hom.: 1197 Cov.: 31

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0976

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.0893 AC: 15 AN: 168 Hom.: 1 Cov.: 0 AF XY: 0.101 AC XY: 14 AN XY: 138

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.125

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0714

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.109 AC: 16545 AN: 152020 Hom.: 1201 Cov.: 31 AF XY: 0.113 AC XY: 8377 AN XY: 74272

Gnomad4 AFR AF: 0.0301

Gnomad4 AMR AF: 0.0976

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.136

Alfa AF: 0.122 Hom.: 1416

Bravo AF: 0.103

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

LINC-PINT-related disorder Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 26, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.1
DANN	Benign	0.87
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3800567; hg19: chr7-130791653;