5-4365355-G-A

Position:

• chr5-4365355-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 0.456 in 151,974 control chromosomes in the GnomAD database, including 16,351 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 0.46 (16351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

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 (EAS) allele frequency at 95% confidence interval = 0.652 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: 0.456 AC: 69236 AN: 151856 Hom.: 16354 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.456 AC: 69246 AN: 151974 Hom.: 16351 Cov.: 32 AF XY: 0.457 AC XY: 33904 AN XY: 74268

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.447

Alfa AF: 0.476 Hom.: 4412

Bravo AF: 0.440

Asia WGS AF: 0.533 AC: 1852 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.076
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs261119; hg19: chr5-4365468;