chr1-233412585-C-G

Position:

• chr1-233412585-C-G

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 0.163 in 152,164 control chromosomes in the GnomAD database, including 2,163 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 (2163 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 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: 0.163 AC: 24823 AN: 152046 Hom.: 2161 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.163 AC: 24837 AN: 152164 Hom.: 2163 Cov.: 33 AF XY: 0.164 AC XY: 12224 AN XY: 74384

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0419

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.159

Alfa AF: 0.152 Hom.: 224

Bravo AF: 0.154

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.8
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17205291; hg19: chr1-233548331;