4-45569697-A-G

Position:

• chr4-45569697-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 0.891 in 152,196 control chromosomes in the GnomAD database, including 60,492 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 0.89 (60492 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.891 AC: 135476 AN: 152078 Hom.: 60459 Cov.: 33

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.891 AC: 135565 AN: 152196 Hom.: 60492 Cov.: 33 AF XY: 0.893 AC XY: 66452 AN XY: 74412

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.924

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.895

Alfa AF: 0.898 Hom.: 7163

Bravo AF: 0.890

Asia WGS AF: 0.958 AC: 3329 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs840187; hg19: chr4-45571714;