1-236793823-G-T

Variant names:

• chr1-236793823-G-T
• rs16834388

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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

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

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.346

Alfa AF: 0.362 Hom.: 3884

Bravo AF: 0.343

Asia WGS AF: 0.365 AC: 1267 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16834388; hg19: chr1-236957123;