chr1-236793823-G-T

Variant names:

• chr1-236793823-G-T
• rs16834388

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 0.35 in 151,320 control chromosomes in the GnomAD database, including 9,945 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 0.35 (9945 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 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: 0.350 AC: 52866 AN: 151206 Hom.: 9942 Cov.: 30

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.350 AC: 52895 AN: 151320 Hom.: 9945 Cov.: 30 AF XY: 0.352 AC XY: 26005 AN XY: 73924

African (AFR) AF: 0.205 AC: 8451 AN: 41196

American (AMR) AF: 0.408 AC: 6208 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2173 AN: 5158

South Asian (SAS) AF: 0.327 AC: 1567 AN: 4798

European-Finnish (FIN) AF: 0.446 AC: 4615 AN: 10348

Middle Eastern (MID) AF: 0.328 AC: 95 AN: 290

European-Non Finnish (NFE) AF: 0.405 AC: 27448 AN: 67856

Other (OTH) AF: 0.346 AC: 722 AN: 2088

Alfa AF: 0.370 Hom.: 6290

Bravo AF: 0.343

Asia WGS AF: 0.365 AC: 1267 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.0
DANN	Benign	0.79
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs16834388; hg19: chr1-236957123;