chr18-28989937-G-A

Variant names:

• chr18-28989937-G-A
• rs9964679

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 0.467 in 139,154 control chromosomes in the GnomAD database, including 15,172 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 0.47 (15172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 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: 0.466 AC: 64825 AN: 139022 Hom.: 15135 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.467 AC: 64918 AN: 139154 Hom.: 15172 Cov.: 32 AF XY: 0.475 AC XY: 32072 AN XY: 67544

African (AFR) AF: 0.640 AC: 25306 AN: 39548

American (AMR) AF: 0.528 AC: 7133 AN: 13504

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 970 AN: 3194

East Asian (EAS) AF: 0.592 AC: 2868 AN: 4846

South Asian (SAS) AF: 0.545 AC: 2312 AN: 4244

European-Finnish (FIN) AF: 0.405 AC: 3544 AN: 8756

Middle Eastern (MID) AF: 0.398 AC: 98 AN: 246

European-Non Finnish (NFE) AF: 0.349 AC: 21669 AN: 62150

Other (OTH) AF: 0.433 AC: 798 AN: 1842

Alfa AF: 0.350 Hom.: 17328

Bravo AF: 0.439

Asia WGS AF: 0.511 AC: 1777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.69
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs9964679; hg19: chr18-26569901;