rs241212

Variant names:

• chr1-4571206-G-T
• rs241212

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 0.265 in 152,042 control chromosomes in the GnomAD database, including 6,042 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 0.27 (6042 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40281 AN: 151924 Hom.: 6041 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.265 AC: 40297 AN: 152042 Hom.: 6042 Cov.: 32 AF XY: 0.261 AC XY: 19399 AN XY: 74332

African (AFR) AF: 0.172 AC: 7136 AN: 41484

American (AMR) AF: 0.219 AC: 3339 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3466

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5178

South Asian (SAS) AF: 0.187 AC: 900 AN: 4820

European-Finnish (FIN) AF: 0.336 AC: 3542 AN: 10550

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23293 AN: 67956

Other (OTH) AF: 0.275 AC: 579 AN: 2104

Alfa AF: 0.312 Hom.: 9843

Bravo AF: 0.253

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.33
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs241212; hg19: chr1-4631266;