chr2-28423934-G-A

Position:

• chr2-28423934-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 0.348 in 152,022 control chromosomes in the GnomAD database, including 9,739 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 0.35 (9739 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 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: 0.348 AC: 52866 AN: 151904 Hom.: 9730 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.348 AC: 52897 AN: 152022 Hom.: 9739 Cov.: 32 AF XY: 0.338 AC XY: 25155 AN XY: 74320

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.330

Alfa AF: 0.368 Hom.: 14126

Bravo AF: 0.342

Asia WGS AF: 0.129 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6547853; hg19: chr2-28646801;