chr3-52218953-T-C

Variant names:

• chr3-52218953-T-C
• rs352162
• ENST00000624096.1:n.60A>G

Variant summary

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

The ENST00000624096.1(ENSG00000280003):​n.60A>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 0.543 in 153,270 control chromosomes in the GnomAD database, including 22,765 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 0.54 (22570 hom., cov: 30)
  • Exomes 𝑓: 0.48 (195 hom.)
• Consequence: ENSG00000280003 ENST00000624096.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

Genes affected

ENSG00000280003 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000280003	ENST00000624096.1	n.60A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82365 AN: 151674 Hom.: 22549 Cov.: 30

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.538

GnomAD4 exome AF: 0.483 AC: 714 AN: 1478 Hom.: 195 Cov.: 0 AF XY: 0.500 AC XY: 393 AN XY: 786

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.667

Gnomad4 ASJ exome AF: 0.300

Gnomad4 EAS exome AF: 0.425

Gnomad4 SAS exome AF: 0.438

Gnomad4 FIN exome AF: 0.455

Gnomad4 NFE exome AF: 0.496

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.543 AC: 82436 AN: 151792 Hom.: 22570 Cov.: 30 AF XY: 0.538 AC XY: 39888 AN XY: 74162

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.539

Alfa AF: 0.545 Hom.: 7158

Bravo AF: 0.549

Asia WGS AF: 0.450 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs352162; hg19: chr3-52252969;