rs2678919

Positions:

• chr2-57897224-G-A

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 0.321 in 151,914 control chromosomes in the GnomAD database, including 7,846 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 0.32 (7846 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48722 AN: 151792 Hom.: 7841 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.321 AC: 48758 AN: 151914 Hom.: 7846 Cov.: 32 AF XY: 0.321 AC XY: 23823 AN XY: 74266

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.319

Alfa AF: 0.307 Hom.: 14771

Bravo AF: 0.324

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2678919; hg19: chr2-58124359;