7-130976069-C-G

Position:

• chr7-130976069-C-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC-PINT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC-PINT	NR_015431.2	n.1452+7984G>C		intron_variant
LINC-PINT	NR_024153.2	n.418+7984G>C		intron_variant
LINC-PINT	NR_109850.1	n.1576+7984G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC-PINT	ENST00000433079.5	n.418+7984G>C		intron_variant		1
LINC-PINT	ENST00000423414.5	n.401+7984G>C		intron_variant		4
LINC-PINT	ENST00000431189.2	n.583+7984G>C		intron_variant		3

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

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.636

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs205737; hg19: chr7-130660828;