rs1556876

Variant names:

• chr20-49099914-A-C
• rs1556876

Your query was ambiguous. Multiple possible variants found:

• chr20-49099914-A-C
• chr20-49099914-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 0.21 in 152,050 control chromosomes in the GnomAD database, including 3,510 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 0.21 (3510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.238 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: 0.211 AC: 31988 AN: 151932 Hom.: 3508 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.210 AC: 32004 AN: 152050 Hom.: 3510 Cov.: 32 AF XY: 0.205 AC XY: 15243 AN XY: 74324

African (AFR) AF: 0.207 AC: 8570 AN: 41438

American (AMR) AF: 0.169 AC: 2579 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 605 AN: 3472

East Asian (EAS) AF: 0.0505 AC: 261 AN: 5168

South Asian (SAS) AF: 0.0900 AC: 434 AN: 4824

European-Finnish (FIN) AF: 0.226 AC: 2387 AN: 10556

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16376 AN: 67986

Other (OTH) AF: 0.172 AC: 364 AN: 2116

Alfa AF: 0.224 Hom.: 16932

Bravo AF: 0.206

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs1556876; hg19: chr20-47716451;