rs999051

Variant names:

• chr1-203442731-T-C
• rs999051

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 0.155 in 152,232 control chromosomes in the GnomAD database, including 1,913 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 (1913 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 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: 0.155 AC: 23644 AN: 152114 Hom.: 1910 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.155 AC: 23668 AN: 152232 Hom.: 1913 Cov.: 33 AF XY: 0.159 AC XY: 11838 AN XY: 74416

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.143

Alfa AF: 0.142 Hom.: 3008

Bravo AF: 0.149

Asia WGS AF: 0.198 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs999051; hg19: chr1-203411859; COSMIC: COSV60018358;