1-203207759-C-A

Variant names:

• chr1-203207759-C-A
• rs2494303

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 0.185 in 152,124 control chromosomes in the GnomAD database, including 3,582 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 (3582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 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: 0.185 AC: 28170 AN: 152006 Hom.: 3571 Cov.: 32

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.185 AC: 28189 AN: 152124 Hom.: 3582 Cov.: 32 AF XY: 0.194 AC XY: 14406 AN XY: 74360

Gnomad4 AFR AF: 0.0555

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.210

Alfa AF: 0.0796 Hom.: 105

Bravo AF: 0.181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2494303; hg19: chr1-203176887;