rs1827924

Variant names:

• chr2-227805019-A-G
• rs1827924

Your query was ambiguous. Multiple possible variants found:

• chr2-227805019-A-G
• chr2-227805019-A-T

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 0.358 in 152,052 control chromosomes in the GnomAD database, including 10,052 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 0.36 (10052 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.827
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 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: 0.358 AC: 54432 AN: 151934 Hom.: 10040 Cov.: 33

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.358 AC: 54482 AN: 152052 Hom.: 10052 Cov.: 33 AF XY: 0.357 AC XY: 26525 AN XY: 74328

African (AFR) AF: 0.452 AC: 18734 AN: 41460

American (AMR) AF: 0.334 AC: 5101 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3470

East Asian (EAS) AF: 0.294 AC: 1520 AN: 5178

South Asian (SAS) AF: 0.348 AC: 1680 AN: 4828

European-Finnish (FIN) AF: 0.284 AC: 2999 AN: 10564

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21700 AN: 67962

Other (OTH) AF: 0.372 AC: 785 AN: 2110

Alfa AF: 0.339 Hom.: 16646

Bravo AF: 0.366

Asia WGS AF: 0.305 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.80
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs1827924; hg19: chr2-228669735;