rs1919484

Variant names:

• chr8-20012165-G-A
• rs1919484

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 0.228 in 152,064 control chromosomes in the GnomAD database, including 4,142 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 0.23 (4142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 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: 0.228 AC: 34647 AN: 151946 Hom.: 4144 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.228 AC: 34638 AN: 152064 Hom.: 4142 Cov.: 32 AF XY: 0.228 AC XY: 16911 AN XY: 74328

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.234

Alfa AF: 0.232 Hom.: 989

Bravo AF: 0.222

Asia WGS AF: 0.233 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1919484; hg19: chr8-19869676;