rs9304408

Variant names:

• chr18-51147986-C-T
• rs9304408

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 0.383 in 152,028 control chromosomes in the GnomAD database, including 11,447 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 0.38 (11447 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 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: 0.383 AC: 58132 AN: 151910 Hom.: 11444 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.383 AC: 58171 AN: 152028 Hom.: 11447 Cov.: 33 AF XY: 0.384 AC XY: 28535 AN XY: 74296

African (AFR) AF: 0.301 AC: 12492 AN: 41456

American (AMR) AF: 0.459 AC: 6999 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1473 AN: 3466

East Asian (EAS) AF: 0.488 AC: 2526 AN: 5180

South Asian (SAS) AF: 0.411 AC: 1983 AN: 4822

European-Finnish (FIN) AF: 0.360 AC: 3789 AN: 10534

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

European-Non Finnish (NFE) AF: 0.408 AC: 27719 AN: 67990

Other (OTH) AF: 0.381 AC: 805 AN: 2114

Alfa AF: 0.400 Hom.: 54401

Bravo AF: 0.383

Asia WGS AF: 0.402 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9304408; hg19: chr18-48674356;