rs999051

Variant names:

• chr1-203442731-T-C
• rs999051

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.167 AC: 6946 AN: 41548

American (AMR) AF: 0.115 AC: 1762 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 585 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1289 AN: 5172

South Asian (SAS) AF: 0.175 AC: 842 AN: 4818

European-Finnish (FIN) AF: 0.209 AC: 2216 AN: 10604

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9460 AN: 68010

Other (OTH) AF: 0.143 AC: 302 AN: 2108

Alfa AF: 0.144 Hom.: 6306

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
PhyloP100		-0.24

Splicing

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

Other links and lift over

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