rs157927

Positions:

• chr7-130896461-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110473.1(LINC-PINT):​n.404-12065C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.908 in 152,240 control chromosomes in the GnomAD database, including 62,988 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 0.91 (62988 hom., cov: 31)
• Consequence: LINC-PINT NR_110473.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC-PINT	NR_110473.1	n.404-12065C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC-PINT	ENST00000642963.1	n.514-12065C>T		intron_variant, non_coding_transcript_variant
LINC00513	ENST00000653887.1	n.145-18501G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.908 AC: 138093 AN: 152122 Hom.: 62956 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.908 AC: 138187 AN: 152240 Hom.: 62988 Cov.: 31 AF XY: 0.909 AC XY: 67656 AN XY: 74440

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.950

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.914

Alfa AF: 0.920 Hom.: 8737

Bravo AF: 0.904

Asia WGS AF: 0.921 AC: 3205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs157927; hg19: chr7-130581220;