rs409783

Positions:

• chr8-23838390-G-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.23838390G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;