chr5-1447726-G-A

Position:

• chr5-1447726-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 0.208 in 152,088 control chromosomes in the GnomAD database, including 3,769 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 0.21 (3769 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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 (SAS) allele frequency at 95% confidence interval = 0.269 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: 0.208 AC: 31614 AN: 151972 Hom.: 3757 Cov.: 33

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.208 AC: 31646 AN: 152088 Hom.: 3769 Cov.: 33 AF XY: 0.210 AC XY: 15618 AN XY: 74336

Gnomad4 AFR AF: 0.0889

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.220

Alfa AF: 0.242 Hom.: 1417

Bravo AF: 0.194

Asia WGS AF: 0.217 AC: 750 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	0.084
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2550956; hg19: chr5-1447841;