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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.270 AC: 11192 AN: 41480

American (AMR) AF: 0.430 AC: 6561 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1556 AN: 3466

East Asian (EAS) AF: 0.377 AC: 1947 AN: 5158

South Asian (SAS) AF: 0.371 AC: 1788 AN: 4816

European-Finnish (FIN) AF: 0.446 AC: 4702 AN: 10552

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31306 AN: 67958

Other (OTH) AF: 0.403 AC: 850 AN: 2110

Alfa AF: 0.425 Hom.: 11094

Bravo AF: 0.393

Asia WGS AF: 0.387 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.54
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs4892138; hg19: chr18-71458785;