rs17724512

Variant names:

• chr20-6683530-C-A
• rs17724512

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0631 in 152,246 control chromosomes in the GnomAD database, including 393 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 0.063 (393 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.14
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.087 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: 0.0631 AC: 9605 AN: 152128 Hom.: 394 Cov.: 33

Gnomad AFR AF: 0.0200

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0251

Gnomad FIN AF: 0.0694

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0631 AC: 9603 AN: 152246 Hom.: 393 Cov.: 33 AF XY: 0.0622 AC XY: 4631 AN XY: 74430

African (AFR) AF: 0.0200 AC: 831 AN: 41550

American (AMR) AF: 0.0695 AC: 1062 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.0249 AC: 120 AN: 4822

European-Finnish (FIN) AF: 0.0694 AC: 735 AN: 10596

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0889 AC: 6048 AN: 68018

Other (OTH) AF: 0.0833 AC: 176 AN: 2114

Alfa AF: 0.0802 Hom.: 297

Bravo AF: 0.0612

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	15
DANN	Benign	0.58
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs17724512; hg19: chr20-6664177;