1-239355766-G-A

Variant names:

• chr1-239355766-G-A
• rs12036333

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 0.16 in 152,116 control chromosomes in the GnomAD database, including 2,564 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 0.16 (2564 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.35 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: 0.160 AC: 24391 AN: 151998 Hom.: 2570 Cov.: 32

Gnomad AFR AF: 0.0394

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.160 AC: 24389 AN: 152116 Hom.: 2564 Cov.: 32 AF XY: 0.164 AC XY: 12186 AN XY: 74314

African (AFR) AF: 0.0393 AC: 1631 AN: 41536

American (AMR) AF: 0.283 AC: 4317 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 845 AN: 3468

East Asian (EAS) AF: 0.364 AC: 1879 AN: 5166

South Asian (SAS) AF: 0.158 AC: 759 AN: 4818

European-Finnish (FIN) AF: 0.186 AC: 1960 AN: 10546

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12401 AN: 68002

Other (OTH) AF: 0.168 AC: 354 AN: 2108

Alfa AF: 0.184 Hom.: 4484

Bravo AF: 0.170

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.47
DANN	Benign	0.48
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs12036333; hg19: chr1-239519066;