18-57590927-T-G

Variant names:

• chr18-57590927-T-G
• rs434397

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 0.759 in 152,046 control chromosomes in the GnomAD database, including 44,054 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 0.76 (44054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 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: 0.759 AC: 115385 AN: 151928 Hom.: 44023 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.759 AC: 115471 AN: 152046 Hom.: 44054 Cov.: 32 AF XY: 0.760 AC XY: 56485 AN XY: 74316

African (AFR) AF: 0.706 AC: 29247 AN: 41420

American (AMR) AF: 0.818 AC: 12500 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2821 AN: 3468

East Asian (EAS) AF: 0.890 AC: 4589 AN: 5158

South Asian (SAS) AF: 0.815 AC: 3931 AN: 4822

European-Finnish (FIN) AF: 0.690 AC: 7317 AN: 10600

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.775 AC: 52714 AN: 67984

Other (OTH) AF: 0.769 AC: 1620 AN: 2108

Alfa AF: 0.765 Hom.: 5528

Bravo AF: 0.767

Asia WGS AF: 0.836 AC: 2905 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.59
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs434397; hg19: chr18-55258159;