rs1827924

chr2-227805019-A-Gchr2-227805019-A-T

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 0.358 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.372

Alfa AF: 0.336 Hom.: 11783

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1827924; hg19: chr2-228669735;