chr1-203192233-G-A

Variant names:

• chr1-203192233-G-A
• rs4950930

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 0.0338 in 152,290 control chromosomes in the GnomAD database, including 114 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 0.034 (114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0588 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0338 AC: 5145 AN: 152172 Hom.: 112 Cov.: 32

Gnomad AFR AF: 0.00891

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0466

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0338 AC: 5147 AN: 152290 Hom.: 114 Cov.: 32 AF XY: 0.0338 AC XY: 2515 AN XY: 74458

African (AFR) AF: 0.00888 AC: 369 AN: 41554

American (AMR) AF: 0.0376 AC: 575 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.0647 AC: 312 AN: 4822

European-Finnish (FIN) AF: 0.0451 AC: 478 AN: 10600

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0466 AC: 3169 AN: 68026

Other (OTH) AF: 0.0336 AC: 71 AN: 2116

Alfa AF: 0.0357 Hom.: 15

Bravo AF: 0.0310

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.31
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs4950930; hg19: chr1-203161361;