rs735266

Variant names:

• chr22-35372070-T-A
• rs735266
• ENST00000632196.1:n.-104T>A

Variant summary

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

The ENST00000632196.1(ENSG00000282602):​n.-104T>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,302 control chromosomes in the GnomAD database, including 7,729 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 0.31 (7727 hom., cov: 28)
  • Exomes 𝑓: 0.31 (2 hom.)
• Consequence: ENSG00000282602 ENST00000632196.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408

Genes affected

ENSG00000282602 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 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
ENSG00000282602	ENST00000632196.1	n.-104T>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.311 AC: 46990 AN: 151114 Hom.: 7735 Cov.: 28

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.332

GnomAD4 exome AF: 0.309 AC: 21 AN: 68 Hom.: 2 AF XY: 0.300 AC XY: 15 AN XY: 50

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.311 AC: 46983 AN: 151234 Hom.: 7727 Cov.: 28 AF XY: 0.310 AC XY: 22925 AN XY: 73856

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.331

Alfa AF: 0.341 Hom.: 1182

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.8
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs735266; hg19: chr22-35768063;