5-1446274-A-G

Position:

• chr5-1446274-A-G

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 0.505 in 152,014 control chromosomes in the GnomAD database, including 20,422 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 0.50 (20422 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.594 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: 0.505 AC: 76686 AN: 151896 Hom.: 20401 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.505 AC: 76765 AN: 152014 Hom.: 20422 Cov.: 33 AF XY: 0.504 AC XY: 37452 AN XY: 74308

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.525

Alfa AF: 0.555 Hom.: 8483

Bravo AF: 0.489

Asia WGS AF: 0.367 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2652511; hg19: chr5-1446389;