1-236793823-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;