rs4892138

Variant names:

• chr18-73791550-A-G
• rs4892138

Your query was ambiguous. Multiple possible variants found:

• chr18-73791550-A-G
• chr18-73791550-A-T

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 0.398 in 152,012 control chromosomes in the GnomAD database, including 12,572 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 0.40 (12572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 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: 0.398 AC: 60456 AN: 151894 Hom.: 12572 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.398 AC: 60481 AN: 152012 Hom.: 12572 Cov.: 32 AF XY: 0.397 AC XY: 29513 AN XY: 74308

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.403

Alfa AF: 0.423 Hom.: 7953

Bravo AF: 0.393

Asia WGS AF: 0.387 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4892138; hg19: chr18-71458785;