20-23795182-T-C

Variant names:

• chr20-23795182-T-C
• rs6049129

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.183 AC: 7592 AN: 41498

American (AMR) AF: 0.278 AC: 4246 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2152 AN: 5174

South Asian (SAS) AF: 0.315 AC: 1520 AN: 4826

European-Finnish (FIN) AF: 0.282 AC: 2981 AN: 10560

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24299 AN: 67966

Other (OTH) AF: 0.325 AC: 687 AN: 2112

Alfa AF: 0.338 Hom.: 36231

Bravo AF: 0.292

Asia WGS AF: 0.364 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.0
DANN	Benign	0.29
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs6049129; hg19: chr20-23775819;