rs728504

Variant names:

• chr20-57760110-T-C
• rs728504

Your query was ambiguous. Multiple possible variants found:

• chr20-57760110-T-C
• chr20-57760110-T-G

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 0.37 in 151,976 control chromosomes in the GnomAD database, including 13,958 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 0.37 (13958 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 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: 0.370 AC: 56136 AN: 151858 Hom.: 13929 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.370 AC: 56226 AN: 151976 Hom.: 13958 Cov.: 32 AF XY: 0.372 AC XY: 27633 AN XY: 74296

African (AFR) AF: 0.651 AC: 26969 AN: 41420

American (AMR) AF: 0.361 AC: 5515 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3466

East Asian (EAS) AF: 0.828 AC: 4264 AN: 5148

South Asian (SAS) AF: 0.423 AC: 2034 AN: 4806

European-Finnish (FIN) AF: 0.170 AC: 1801 AN: 10582

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13782 AN: 67964

Other (OTH) AF: 0.368 AC: 775 AN: 2108

Alfa AF: 0.287 Hom.: 12629

Bravo AF: 0.397

Asia WGS AF: 0.630 AC: 2191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs728504; hg19: chr20-56335166;