rs958523

Variant names:

• chr20-39953703-G-A
• rs958523

Your query was ambiguous. Multiple possible variants found:

• chr20-39953703-G-A
• chr20-39953703-G-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 0.333 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.307

Alfa AF: 0.322 Hom.: 10576

Bravo AF: 0.330

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs958523; hg19: chr20-38582345;