rs1877751

Variant names:

• chr20-59392851-A-G
• rs1877751

Your query was ambiguous. Multiple possible variants found:

• chr20-59392851-A-G
• chr20-59392851-A-T

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 0.309 in 152,070 control chromosomes in the GnomAD database, including 8,828 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 (8828 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.309 AC: 46940 AN: 151952 Hom.: 8801 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.309 AC: 47001 AN: 152070 Hom.: 8828 Cov.: 32 AF XY: 0.313 AC XY: 23256 AN XY: 74336

African (AFR) AF: 0.172 AC: 7133 AN: 41498

American (AMR) AF: 0.517 AC: 7891 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1236 AN: 3468

East Asian (EAS) AF: 0.823 AC: 4244 AN: 5156

South Asian (SAS) AF: 0.412 AC: 1981 AN: 4814

European-Finnish (FIN) AF: 0.243 AC: 2572 AN: 10586

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20901 AN: 67968

Other (OTH) AF: 0.347 AC: 730 AN: 2106

Alfa AF: 0.327 Hom.: 30623

Bravo AF: 0.329

Asia WGS AF: 0.599 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	12
DANN	Benign	0.61
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1877751; hg19: chr20-57967906;