rs6971499

Positions:

• chr7-130995762-T-C

Variant summary

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

The ENST00000433079.5(LINC-PINT):​n.362-11653A>G 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 0.144 in 152,254 control chromosomes in the GnomAD database, including 1,757 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 0.14 (1757 hom., cov: 33)
• Consequence: LINC-PINT ENST00000433079.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC-PINT	NR_015431.2	n.1396-11653A>G		intron_variant, non_coding_transcript_variant
LINC-PINT	NR_024153.2	n.362-11653A>G		intron_variant, non_coding_transcript_variant
LINC-PINT	NR_109850.1	n.1519+6435A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC-PINT	ENST00000642963.1	n.341-11653A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21853 AN: 152136 Hom.: 1759 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.0938

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.144 AC: 21865 AN: 152254 Hom.: 1757 Cov.: 33 AF XY: 0.140 AC XY: 10407 AN XY: 74444

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0994

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0360

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.0938

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.126

Alfa AF: 0.147 Hom.: 1458

Bravo AF: 0.144

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6971499; hg19: chr7-130680521;