chr7-130896461-G-A

Variant names:

• chr7-130896461-G-A
• rs157927
• ENST00000418546.1:n.291-12065C>T

Variant summary

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

The ENST00000418546.1(LINC-PINT):​n.291-12065C>T variant causes a intron 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 ENST00000418546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 1 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=-0.92).
• 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 rank	MANE	Protein	UniProt
LINC-PINT	NR_034120.1	n.404-12065C>T		intron_variant	Intron 2 of 3
LINC-PINT	NR_110472.1	n.404-12065C>T		intron_variant	Intron 2 of 3
LINC-PINT	NR_110473.1	n.404-12065C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC-PINT	ENST00000418546.1	n.291-12065C>T		intron_variant	Intron 2 of 2	4
LINC-PINT	ENST00000432045.6	n.404-12065C>T		intron_variant	Intron 2 of 3	2
LINC-PINT	ENST00000447307.5	n.270-12065C>T		intron_variant	Intron 2 of 3	3

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

African (AFR) AF: 0.819 AC: 33995 AN: 41500

American (AMR) AF: 0.950 AC: 14528 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3055 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5152 AN: 5186

South Asian (SAS) AF: 0.857 AC: 4133 AN: 4822

European-Finnish (FIN) AF: 0.958 AC: 10180 AN: 10622

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.943 AC: 64131 AN: 68030

Other (OTH) AF: 0.914 AC: 1932 AN: 2114

Alfa AF: 0.927 Hom.: 31525

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
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs157927; hg19: chr7-130581220;