4-89858672-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 0.738 in 152,020 control chromosomes in the GnomAD database, including 41,762 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 0.74 (41762 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

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 (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112170 AN: 151900 Hom.: 41745 Cov.: 31

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.738 AC: 112222 AN: 152020 Hom.: 41762 Cov.: 31 AF XY: 0.735 AC XY: 54631 AN XY: 74314

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.716

Alfa AF: 0.759 Hom.: 41975

Bravo AF: 0.732

Asia WGS AF: 0.711 AC: 2469 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.8
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2737026; hg19: chr4-90779823;