rs4273712

Variant names:

• chr6-126643364-A-G
• rs4273712
• ENST00000650727.1:n.1167-21491T>C

Variant summary

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

The ENST00000650727.1(ENSG00000286215):​n.1167-21491T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 399,210 control chromosomes in the GnomAD database, including 17,934 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 0.24 (5356 hom., cov: 32)
  • Exomes 𝑓: 0.30 (12578 hom.)
• Consequence: ENSG00000286215 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

ENSG00000286215 (HGNC:):

PRELID1P1 (HGNC:43886): (PRELID1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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
ENSG00000286215	ENST00000650727.1	n.1167-21491T>C		intron_variant	Intron 9 of 14
ENSG00000286215	ENST00000651326.1	n.694-39899T>C		intron_variant	Intron 3 of 6
ENSG00000286215	ENST00000652545.1	n.1477-21491T>C		intron_variant	Intron 10 of 15
PRELID1P1	ENST00000567272.1	n.-124A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36841 AN: 152054 Hom.: 5354 Cov.: 32

Gnomad AFR AF: 0.0878

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.285

GnomAD4 exome AF: 0.305 AC: 75316 AN: 247038 Hom.: 12578 AF XY: 0.309 AC XY: 40156 AN XY: 130068

Gnomad4 AFR exome AF: 0.105

Gnomad4 AMR exome AF: 0.471

Gnomad4 ASJ exome AF: 0.325

Gnomad4 EAS exome AF: 0.467

Gnomad4 SAS exome AF: 0.381

Gnomad4 FIN exome AF: 0.272

Gnomad4 NFE exome AF: 0.274

Gnomad4 OTH exome AF: 0.301

GnomAD4 genome AF: 0.242 AC: 36850 AN: 152172 Hom.: 5356 Cov.: 32 AF XY: 0.249 AC XY: 18545 AN XY: 74430

Gnomad4 AFR AF: 0.0878

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.282

Alfa AF: 0.278 Hom.: 13798

Bravo AF: 0.250

Asia WGS AF: 0.354 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4273712; hg19: chr6-126964510; COSMIC: COSV69095953;