1-153233575-T-A

Variant names:

• chr1-153233575-T-A
• rs16835086

Variant summary

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

The variant allele was found at a frequency of 0.212 in 152,018 control chromosomes in the GnomAD database, including 3,746 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 0.21 (3746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32208 AN: 151900 Hom.: 3737 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.249

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.212 AC: 32254 AN: 152018 Hom.: 3746 Cov.: 32 AF XY: 0.219 AC XY: 16249 AN XY: 74314

African (AFR) AF: 0.228 AC: 9464 AN: 41426

American (AMR) AF: 0.333 AC: 5078 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1391 AN: 5184

South Asian (SAS) AF: 0.360 AC: 1739 AN: 4824

European-Finnish (FIN) AF: 0.136 AC: 1434 AN: 10550

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11396 AN: 67980

Other (OTH) AF: 0.247 AC: 522 AN: 2114

Alfa AF: 0.0792 Hom.: 94

Bravo AF: 0.224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.61
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs16835086; hg19: chr1-153206051;