7-131002229-G-A

Position:

• chr7-131002229-G-A

Variant summary

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

The ENST00000451786.6(LINC-PINT):​n.1747C>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 0.699 in 150,636 control chromosomes in the GnomAD database, including 36,926 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.70 (36894 hom., cov: 25)
  • Exomes 𝑓: 0.68 (32 hom.)
• Consequence: LINC-PINT ENST00000451786.6 non_coding_transcript_exon
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.580

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 7-131002229-G-A is Benign according to our data. Variant chr7-131002229-G-A is described in ClinVar as [Benign]. Clinvar id is 3059288.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC-PINT	NR_109850.1	n.1487C>T		non_coding_transcript_exon_variant	4/6
LINC-PINT	NR_170175.1	n.1496C>T		non_coding_transcript_exon_variant	4/10
LINC-PINT	NR_015431.2	n.1396-18120C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC-PINT	ENST00000433079.5	n.362-18120C>T		intron_variant		1
LINC-PINT	ENST00000451786.6	n.1747C>T		non_coding_transcript_exon_variant	4/6	2
LINC-PINT	ENST00000642483.2	n.602C>T		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.699 AC: 105122 AN: 150388 Hom.: 36877 Cov.: 25

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.664

GnomAD4 exome AF: 0.681 AC: 94 AN: 138 Hom.: 32 Cov.: 0 AF XY: 0.676 AC XY: 69 AN XY: 102

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.675

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.699 AC: 105182 AN: 150498 Hom.: 36894 Cov.: 25 AF XY: 0.702 AC XY: 51548 AN XY: 73450

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.663

Alfa AF: 0.713 Hom.: 4597

Bravo AF: 0.687

Asia WGS AF: 0.660 AC: 2293 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

Sep 20, 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	5.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1877727; hg19: chr7-130686988;