chr4-89844129-A-G

Position:

• chr4-89844129-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 0.544 in 151,970 control chromosomes in the GnomAD database, including 23,074 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 0.54 (23074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 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: 0.545 AC: 82688 AN: 151850 Hom.: 23069 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.544 AC: 82716 AN: 151970 Hom.: 23074 Cov.: 32 AF XY: 0.544 AC XY: 40392 AN XY: 74274

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.509

Alfa AF: 0.471 Hom.: 5438

Bravo AF: 0.544

Asia WGS AF: 0.650 AC: 2247 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372522; hg19: chr4-90765280;