20-23795182-T-C

Position:

• chr20-23795182-T-C

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 0.298 in 152,096 control chromosomes in the GnomAD database, including 7,298 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 0.30 (7298 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23795182T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45278 AN: 151978 Hom.: 7297 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.298 AC: 45306 AN: 152096 Hom.: 7298 Cov.: 32 AF XY: 0.295 AC XY: 21925 AN XY: 74354

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.325

Alfa AF: 0.347 Hom.: 18211

Bravo AF: 0.292

Asia WGS AF: 0.364 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.0
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6049129; hg19: chr20-23775819;