rs205756

Positions:

• chr7-130896317-G-T

Variant summary

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

The NR_110473.1(LINC-PINT):​n.404-11921C>A 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 0.324 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 NR_110473.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

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=-0.96).
• 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/exons	MANE	UniProt
LINC-PINT	NR_110473.1	n.404-11921C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC-PINT	ENST00000642963.1	n.514-11921C>A		intron_variant, non_coding_transcript_variant
LINC00513	ENST00000653887.1	n.145-18645G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.307

Alfa AF: 0.350 Hom.: 7428

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
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

Publications

LitVar

Other links and lift over

dbSNP: rs205756; hg19: chr7-130581076;