rs10237038

Positions:

• chr7-131006423-C-T

Variant summary

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

The ENST00000433079.5(LINC-PINT):​n.362-22314G>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 0.144 in 151,898 control chromosomes in the GnomAD database, including 1,730 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 (1730 hom., cov: 30)
• Consequence: LINC-PINT ENST00000433079.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC-PINT	NR_015431.2	n.1396-22314G>A		intron_variant, non_coding_transcript_variant
LINC-PINT	NR_024153.2	n.362-22314G>A		intron_variant, non_coding_transcript_variant
LINC-PINT	NR_109850.1	n.1396-4103G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC-PINT	ENST00000642963.1	n.341-22314G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21885 AN: 151778 Hom.: 1731 Cov.: 30

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0533

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0963

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.144 AC: 21898 AN: 151898 Hom.: 1730 Cov.: 30 AF XY: 0.140 AC XY: 10396 AN XY: 74228

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0530

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.0963

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.124

Alfa AF: 0.151 Hom.: 2081

Bravo AF: 0.144

Asia WGS AF: 0.109 AC: 380 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.37
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10237038; hg19: chr7-130691182;