rs987481

Variant names:

• chr20-56238172-T-C
• rs987481

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 0.0623 in 152,230 control chromosomes in the GnomAD database, including 368 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 0.062 (368 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.102 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: 0.0622 AC: 9464 AN: 152112 Hom.: 367 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.0375

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0560

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

GnomAD4 genome AF: 0.0623 AC: 9486 AN: 152230 Hom.: 368 Cov.: 33 AF XY: 0.0654 AC XY: 4865 AN XY: 74424

African (AFR) AF: 0.104 AC: 4337 AN: 41520

American (AMR) AF: 0.101 AC: 1545 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.0376 AC: 195 AN: 5182

South Asian (SAS) AF: 0.0640 AC: 308 AN: 4816

European-Finnish (FIN) AF: 0.0759 AC: 805 AN: 10612

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0286 AC: 1948 AN: 68024

Other (OTH) AF: 0.0554 AC: 117 AN: 2112

Alfa AF: 0.0469 Hom.: 29

Bravo AF: 0.0623

Asia WGS AF: 0.0730 AC: 252 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	6.4
DANN	Benign	0.45
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs987481; hg19: chr20-54813228;