4-89844129-A-G

Variant names:

• chr4-89844129-A-G
• rs1372522

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;