rs10237038

Variant names:

• chr7-131006423-C-T
• rs10237038
• ENST00000433079.5:n.362-22314G>A

Variant summary

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

The ENST00000433079.5(LINC-PINT):​n.362-22314G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 8 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433079.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC-PINT	NR_015431.2		n.1396-22314G>A		intron	N/A
	LINC-PINT	NR_024153.2		n.362-22314G>A		intron	N/A
	LINC-PINT	NR_109850.1		n.1396-4103G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC-PINT	ENST00000433079.5	TSL:1	n.362-22314G>A		intron	N/A
	LINC-PINT	ENST00000423414.5	TSL:4	n.345-22314G>A		intron	N/A
	LINC-PINT	ENST00000431189.3	TSL:3	n.556-22314G>A		intron	N/A

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

African (AFR) AF: 0.160 AC: 6634 AN: 41420

American (AMR) AF: 0.102 AC: 1555 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 504 AN: 3462

East Asian (EAS) AF: 0.0530 AC: 274 AN: 5166

South Asian (SAS) AF: 0.194 AC: 934 AN: 4816

European-Finnish (FIN) AF: 0.0963 AC: 1013 AN: 10514

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10488 AN: 67952

Other (OTH) AF: 0.124 AC: 261 AN: 2110

Alfa AF: 0.149 Hom.: 3084

Bravo AF: 0.144

Asia WGS AF: 0.109 AC: 380 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.37
DANN	Benign	0.60
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10237038; hg19: chr7-130691182;