rs722728

Variant names:

• chr20-40804179-G-A
• rs722728

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 0.307 in 152,038 control chromosomes in the GnomAD database, including 7,487 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 0.31 (7487 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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: 0.307 AC: 46613 AN: 151920 Hom.: 7488 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.307 AC: 46630 AN: 152038 Hom.: 7487 Cov.: 32 AF XY: 0.309 AC XY: 22973 AN XY: 74304

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.347

Alfa AF: 0.343 Hom.: 8577

Bravo AF: 0.300

Asia WGS AF: 0.252 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	0.14
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs722728; hg19: chr20-39432819;