chr18-30516791-T-A

Variant names:

• chr18-30516791-T-A
• rs1443016

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 0.352 in 152,050 control chromosomes in the GnomAD database, including 9,684 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 0.35 (9684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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: 0.352 AC: 53435 AN: 151932 Hom.: 9670 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.352 AC: 53485 AN: 152050 Hom.: 9684 Cov.: 32 AF XY: 0.347 AC XY: 25763 AN XY: 74308

African (AFR) AF: 0.369 AC: 15279 AN: 41436

American (AMR) AF: 0.243 AC: 3720 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3472

East Asian (EAS) AF: 0.166 AC: 858 AN: 5168

South Asian (SAS) AF: 0.313 AC: 1510 AN: 4822

European-Finnish (FIN) AF: 0.392 AC: 4150 AN: 10582

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25806 AN: 67972

Other (OTH) AF: 0.322 AC: 680 AN: 2112

Alfa AF: 0.380 Hom.: 1378

Bravo AF: 0.339

Asia WGS AF: 0.239 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.44
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs1443016; hg19: chr18-28096757;