20-4685463-T-G

Variant names:

• chr20-4685463-T-G
• rs57633656

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 0.0939 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.246 AC: 10196 AN: 41414

American (AMR) AF: 0.0454 AC: 694 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3472

East Asian (EAS) AF: 0.0318 AC: 165 AN: 5188

South Asian (SAS) AF: 0.0602 AC: 290 AN: 4814

European-Finnish (FIN) AF: 0.0717 AC: 761 AN: 10616

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0259 AC: 1763 AN: 67978

Other (OTH) AF: 0.0754 AC: 158 AN: 2096

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs57633656; hg19: chr20-4666109;