rs6025590

chr20-57495449-A-Gchr20-57495449-A-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 0.695 in 152,144 control chromosomes in the GnomAD database, including 37,667 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 0.70 (37667 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105621 AN: 152026 Hom.: 37593 Cov.: 33

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.695 AC: 105756 AN: 152144 Hom.: 37667 Cov.: 33 AF XY: 0.694 AC XY: 51643 AN XY: 74376

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.658

Alfa AF: 0.632 Hom.: 63642

Bravo AF: 0.703

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.41
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6025590; hg19: chr20-56070505;