rs2024791

Variant names:

• chr20-39552181-C-A
• rs2024791

Your query was ambiguous. Multiple possible variants found:

• chr20-39552181-C-A
• chr20-39552181-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 0.0555 in 152,224 control chromosomes in the GnomAD database, including 337 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 0.056 (337 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.906

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.172 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: 0.0555 AC: 8449 AN: 152106 Hom.: 335 Cov.: 32

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0328

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0447

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

GnomAD4 genome AF: 0.0555 AC: 8452 AN: 152224 Hom.: 337 Cov.: 32 AF XY: 0.0599 AC XY: 4457 AN XY: 74412

Gnomad4 AFR AF: 0.0204

Gnomad4 AMR AF: 0.0327

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0576

Gnomad4 OTH AF: 0.0461

Alfa AF: 0.0579 Hom.: 95

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2024791; hg19: chr20-38180824;