18-23664073-G-A

Position:

• chr18-23664073-G-A

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 0.637 in 152,100 control chromosomes in the GnomAD database, including 31,068 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 0.64 (31068 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96734 AN: 151980 Hom.: 31030 Cov.: 33

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.637 AC: 96833 AN: 152100 Hom.: 31068 Cov.: 33 AF XY: 0.636 AC XY: 47255 AN XY: 74334

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.643

Alfa AF: 0.632 Hom.: 28530

Bravo AF: 0.646

Asia WGS AF: 0.518 AC: 1802 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1788776; hg19: chr18-21244037;