rs2293748

Variant names:

• chr7-130944734-T-C
• rs2293748
• ENST00000433079.5:n.690A>G

Variant summary

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

The ENST00000433079.5(LINC-PINT):​n.690A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,062 control chromosomes in the GnomAD database, including 18,446 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 0.48 (18446 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC-PINT ENST00000433079.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC-PINT	NR_015431.2	n.2554A>G		non_coding_transcript_exon_variant	Exon 5 of 5
LINC-PINT	NR_024153.2	n.690A>G		non_coding_transcript_exon_variant	Exon 5 of 5
LINC-PINT	NR_109850.1	n.2678A>G		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC-PINT	ENST00000433079.5	n.690A>G		non_coding_transcript_exon_variant	Exon 5 of 5	1
LINC-PINT	ENST00000431189.3	n.1843A>G		non_coding_transcript_exon_variant	Exon 5 of 5	3
LINC-PINT	ENST00000435523.6	n.650A>G		non_coding_transcript_exon_variant	Exon 5 of 5	3

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73576 AN: 151944 Hom.: 18417 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.448

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.484 AC: 73664 AN: 152062 Hom.: 18446 Cov.: 32 AF XY: 0.489 AC XY: 36382 AN XY: 74336

African (AFR) AF: 0.376 AC: 15590 AN: 41460

American (AMR) AF: 0.438 AC: 6680 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1494 AN: 3472

East Asian (EAS) AF: 0.498 AC: 2581 AN: 5178

South Asian (SAS) AF: 0.589 AC: 2839 AN: 4818

European-Finnish (FIN) AF: 0.668 AC: 7066 AN: 10582

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35913 AN: 67974

Other (OTH) AF: 0.448 AC: 946 AN: 2112

Alfa AF: 0.501 Hom.: 46663

Bravo AF: 0.459

Asia WGS AF: 0.534 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.86
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs2293748; hg19: chr7-130629493;