rs735266

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

ENSG00000282602 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.333 AC: 18 AN: 54

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.192 AC: 7945 AN: 41298

American (AMR) AF: 0.263 AC: 3999 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1319 AN: 3460

East Asian (EAS) AF: 0.429 AC: 2183 AN: 5092

South Asian (SAS) AF: 0.419 AC: 1996 AN: 4760

European-Finnish (FIN) AF: 0.338 AC: 3517 AN: 10418

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 24950 AN: 67716

Other (OTH) AF: 0.331 AC: 691 AN: 2086

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
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs735266; hg19: chr22-35768063;