rs9304608

Variant names:

• chr19-42693429-C-T
• rs9304608

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 0.205 in 152,132 control chromosomes in the GnomAD database, including 5,507 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 0.21 (5507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 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: 0.205 AC: 31138 AN: 152014 Hom.: 5472 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0902

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0845

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.205 AC: 31232 AN: 152132 Hom.: 5507 Cov.: 32 AF XY: 0.202 AC XY: 15009 AN XY: 74360

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0902

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0845

Gnomad4 NFE AF: 0.0869

Gnomad4 OTH AF: 0.185

Alfa AF: 0.115 Hom.: 957

Bravo AF: 0.224

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9304608; hg19: chr19-43197581;