chr8-23596539-C-T

Position:

• chr8-23596539-C-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 0.282 in 151,866 control chromosomes in the GnomAD database, including 6,147 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 0.28 (6147 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42816 AN: 151748 Hom.: 6147 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.282 AC: 42827 AN: 151866 Hom.: 6147 Cov.: 31 AF XY: 0.287 AC XY: 21262 AN XY: 74198

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.275

Alfa AF: 0.277 Hom.: 3170

Bravo AF: 0.274

Asia WGS AF: 0.332 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11776817; hg19: chr8-23454052;