chr5-44879475-G-A

Position:

• chr5-44879475-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 0.551 in 151,912 control chromosomes in the GnomAD database, including 23,402 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 0.55 (23402 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.59 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: 0.551 AC: 83621 AN: 151796 Hom.: 23393 Cov.: 31

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.551 AC: 83648 AN: 151912 Hom.: 23402 Cov.: 31 AF XY: 0.548 AC XY: 40671 AN XY: 74228

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.549

Alfa AF: 0.575 Hom.: 15143

Bravo AF: 0.542

Asia WGS AF: 0.438 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7705343; hg19: chr5-44879577;