chr20-39953703-G-A

Variant names:

• chr20-39953703-G-A
• rs958523

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 0.333 in 152,086 control chromosomes in the GnomAD database, including 8,583 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 0.33 (8583 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50578 AN: 151968 Hom.: 8580 Cov.: 33

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.333 AC: 50609 AN: 152086 Hom.: 8583 Cov.: 33 AF XY: 0.334 AC XY: 24801 AN XY: 74360

African (AFR) AF: 0.362 AC: 14997 AN: 41466

American (AMR) AF: 0.300 AC: 4591 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1568 AN: 5176

South Asian (SAS) AF: 0.205 AC: 991 AN: 4832

European-Finnish (FIN) AF: 0.383 AC: 4042 AN: 10556

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22518 AN: 67984

Other (OTH) AF: 0.307 AC: 649 AN: 2114

Alfa AF: 0.324 Hom.: 13518

Bravo AF: 0.330

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs958523; hg19: chr20-38582345;