rs4890912

chr18-77173985-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 0.6 in 152,086 control chromosomes in the GnomAD database, including 28,254 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 0.60 (28254 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 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: 0.600 AC: 91176 AN: 151968 Hom.: 28251 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.600 AC: 91200 AN: 152086 Hom.: 28254 Cov.: 33 AF XY: 0.603 AC XY: 44849 AN XY: 74358

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.603

Alfa AF: 0.655 Hom.: 66088

Bravo AF: 0.588

Asia WGS AF: 0.685 AC: 2381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.14
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4890912; hg19: chr18-74885941;