rs57633656

chr20-4685463-T-G

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 0.0939 in 152,080 control chromosomes in the GnomAD database, including 1,368 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 0.094 (1368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 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: 0.0937 AC: 14242 AN: 151962 Hom.: 1362 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0454

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.0319

Gnomad SAS AF: 0.0608

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0259

Gnomad OTH AF: 0.0747

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

GnomAD4 genome AF: 0.0939 AC: 14275 AN: 152080 Hom.: 1368 Cov.: 32 AF XY: 0.0941 AC XY: 6996 AN XY: 74370

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.0454

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.0318

Gnomad4 SAS AF: 0.0602

Gnomad4 FIN AF: 0.0717

Gnomad4 NFE AF: 0.0259

Gnomad4 OTH AF: 0.0754

Alfa AF: 0.0630 Hom.: 101

Bravo AF: 0.0990

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.2
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57633656; hg19: chr20-4666109;