chr2-5391399-G-A

Position:

• chr2-5391399-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 0.384 in 152,074 control chromosomes in the GnomAD database, including 12,431 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 0.38 (12431 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.772

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 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: 0.384 AC: 58340 AN: 151956 Hom.: 12437 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.384 AC: 58331 AN: 152074 Hom.: 12431 Cov.: 32 AF XY: 0.381 AC XY: 28301 AN XY: 74344

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.397

Alfa AF: 0.460 Hom.: 17109

Bravo AF: 0.379

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs792106; hg19: chr2-5531532;