chr1-203212234-C-A

Position:

• chr1-203212234-C-A

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 0.19 in 152,200 control chromosomes in the GnomAD database, including 3,650 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 0.19 (3650 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 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: 0.190 AC: 28895 AN: 152082 Hom.: 3639 Cov.: 33

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.190 AC: 28922 AN: 152200 Hom.: 3650 Cov.: 33 AF XY: 0.198 AC XY: 14750 AN XY: 74410

Gnomad4 AFR AF: 0.0657

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.215

Alfa AF: 0.212 Hom.: 7512

Bravo AF: 0.186

Asia WGS AF: 0.454 AC: 1577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12141375; hg19: chr1-203181362;