18-30405513-T-G

Position:

• chr18-30405513-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0304 in 152,296 control chromosomes in the GnomAD database, including 91 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 0.030 (91 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30405513T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286605	ENST00000657542.1	n.528-7114T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0304 AC: 4629 AN: 152178 Hom.: 92 Cov.: 33

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0484

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.0546

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0313

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0304 AC: 4623 AN: 152296 Hom.: 91 Cov.: 33 AF XY: 0.0306 AC XY: 2281 AN XY: 74462

Gnomad4 AFR AF: 0.0143

Gnomad4 AMR AF: 0.0483

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.0863

Gnomad4 SAS AF: 0.0543

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0313

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.00961 Hom.: 3

Bravo AF: 0.0322

Asia WGS AF: 0.0880 AC: 306 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4799964; hg19: chr18-27985479;