18-59913320-G-T

Variant names:

• chr18-59913320-G-T
• rs12454115

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 0.332 in 152,008 control chromosomes in the GnomAD database, including 8,755 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 0.33 (8755 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 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: 0.332 AC: 50462 AN: 151890 Hom.: 8746 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.332 AC: 50500 AN: 152008 Hom.: 8755 Cov.: 32 AF XY: 0.329 AC XY: 24479 AN XY: 74306

African (AFR) AF: 0.261 AC: 10799 AN: 41434

American (AMR) AF: 0.353 AC: 5399 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1264 AN: 5156

South Asian (SAS) AF: 0.336 AC: 1621 AN: 4820

European-Finnish (FIN) AF: 0.279 AC: 2957 AN: 10582

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25541 AN: 67956

Other (OTH) AF: 0.377 AC: 795 AN: 2110

Alfa AF: 0.367 Hom.: 32784

Bravo AF: 0.336

Asia WGS AF: 0.313 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.81
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs12454115; hg19: chr18-57580552;