chr5-44299896-G-A

Position:

• chr5-44299896-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 0.284 in 151,902 control chromosomes in the GnomAD database, including 6,181 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 0.28 (6181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.782

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.336 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: 0.284 AC: 43110 AN: 151782 Hom.: 6183 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.284 AC: 43133 AN: 151902 Hom.: 6181 Cov.: 32 AF XY: 0.281 AC XY: 20842 AN XY: 74216

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.306

Alfa AF: 0.299 Hom.: 4713

Bravo AF: 0.288

Asia WGS AF: 0.270 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	16
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9292903; hg19: chr5-44299998;