18-49464790-A-G

Variant names:

• chr18-49464790-A-G
• rs8099594

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 0.407 in 152,034 control chromosomes in the GnomAD database, including 13,024 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 0.41 (13024 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 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: 0.407 AC: 61887 AN: 151916 Hom.: 13014 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.407 AC: 61926 AN: 152034 Hom.: 13024 Cov.: 32 AF XY: 0.408 AC XY: 30344 AN XY: 74318

African (AFR) AF: 0.501 AC: 20775 AN: 41442

American (AMR) AF: 0.361 AC: 5521 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1520 AN: 3472

East Asian (EAS) AF: 0.572 AC: 2954 AN: 5162

South Asian (SAS) AF: 0.411 AC: 1982 AN: 4822

European-Finnish (FIN) AF: 0.387 AC: 4091 AN: 10560

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23864 AN: 67978

Other (OTH) AF: 0.397 AC: 839 AN: 2112

Alfa AF: 0.369 Hom.: 32679

Bravo AF: 0.414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.87
DANN	Benign	0.78
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs8099594; hg19: chr18-46991160;