18-43145430-A-G

Variant names:

• chr18-43145430-A-G
• rs1878680

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 0.44 in 152,000 control chromosomes in the GnomAD database, including 15,240 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 0.44 (15240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• 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 (AFR) allele frequency at 95% confidence interval = 0.543 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: 0.440 AC: 66864 AN: 151882 Hom.: 15213 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.440 AC: 66946 AN: 152000 Hom.: 15240 Cov.: 32 AF XY: 0.440 AC XY: 32707 AN XY: 74292

African (AFR) AF: 0.549 AC: 22766 AN: 41446

American (AMR) AF: 0.478 AC: 7293 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3468

East Asian (EAS) AF: 0.497 AC: 2562 AN: 5152

South Asian (SAS) AF: 0.302 AC: 1459 AN: 4828

European-Finnish (FIN) AF: 0.433 AC: 4576 AN: 10578

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25791 AN: 67962

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.393 Hom.: 38424

Bravo AF: 0.453

Asia WGS AF: 0.411 AC: 1428 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	0.87
DANN	Benign	0.55
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1878680; hg19: chr18-40725395;