rs205756

Variant names:

• chr7-130896317-G-T
• rs205756
• ENST00000418546.1:n.291-11921C>A

Variant summary

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

The ENST00000418546.1(LINC-PINT):​n.291-11921C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,064 control chromosomes in the GnomAD database, including 8,882 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 0.32 (8882 hom., cov: 32)
• Consequence: LINC-PINT ENST00000418546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC-PINT	NR_034120.1	n.404-11921C>A		intron_variant	Intron 2 of 3
LINC-PINT	NR_110472.1	n.404-11921C>A		intron_variant	Intron 2 of 3
LINC-PINT	NR_110473.1	n.404-11921C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC-PINT	ENST00000418546.1	n.291-11921C>A		intron_variant	Intron 2 of 2	4
LINC-PINT	ENST00000432045.6	n.404-11921C>A		intron_variant	Intron 2 of 3	2
LINC-PINT	ENST00000447307.5	n.270-11921C>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49282 AN: 151946 Hom.: 8882 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.324 AC: 49288 AN: 152064 Hom.: 8882 Cov.: 32 AF XY: 0.327 AC XY: 24333 AN XY: 74338

African (AFR) AF: 0.191 AC: 7916 AN: 41492

American (AMR) AF: 0.266 AC: 4068 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 960 AN: 3472

East Asian (EAS) AF: 0.397 AC: 2047 AN: 5162

South Asian (SAS) AF: 0.348 AC: 1677 AN: 4818

European-Finnish (FIN) AF: 0.493 AC: 5212 AN: 10566

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26452 AN: 67954

Other (OTH) AF: 0.307 AC: 648 AN: 2110

Alfa AF: 0.341 Hom.: 9884

Bravo AF: 0.297

Asia WGS AF: 0.367 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.40
DANN	Benign	0.55
PhyloP100		-0.55
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs205756; hg19: chr7-130581076;