rs409783

Variant names:

• chr8-23838390-G-T
• rs409783

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 0.393 in 151,896 control chromosomes in the GnomAD database, including 12,039 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 0.39 (12039 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.483 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: 0.393 AC: 59676 AN: 151778 Hom.: 12019 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.393 AC: 59733 AN: 151896 Hom.: 12039 Cov.: 31 AF XY: 0.394 AC XY: 29275 AN XY: 74256

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.396

Alfa AF: 0.368 Hom.: 14762

Bravo AF: 0.409

Asia WGS AF: 0.394 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs409783; hg19: chr8-23695903; COSMIC: COSV51689404;