1-233602658-A-C

Position:

• chr1-233602658-A-C

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 0.14 in 152,252 control chromosomes in the GnomAD database, including 1,758 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 0.14 (1758 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21362 AN: 152134 Hom.: 1758 Cov.: 33

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.0979

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.140 AC: 21373 AN: 152252 Hom.: 1758 Cov.: 33 AF XY: 0.139 AC XY: 10335 AN XY: 74442

Gnomad4 AFR AF: 0.0589

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.0979

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.148

Alfa AF: 0.171 Hom.: 3149

Bravo AF: 0.144

Asia WGS AF: 0.156 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.74
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12119367; hg19: chr1-233738404;