rs1555439

Variant names:

• chr20-54192757-T-G
• rs1555439

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 0.821 in 152,102 control chromosomes in the GnomAD database, including 51,605 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 0.82 (51605 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 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: 0.821 AC: 124742 AN: 151984 Hom.: 51541 Cov.: 31

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.821 AC: 124871 AN: 152102 Hom.: 51605 Cov.: 31 AF XY: 0.819 AC XY: 60883 AN XY: 74376

African (AFR) AF: 0.913 AC: 37872 AN: 41488

American (AMR) AF: 0.823 AC: 12585 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2512 AN: 3466

East Asian (EAS) AF: 0.848 AC: 4390 AN: 5178

South Asian (SAS) AF: 0.825 AC: 3982 AN: 4824

European-Finnish (FIN) AF: 0.720 AC: 7620 AN: 10576

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53237 AN: 67970

Other (OTH) AF: 0.795 AC: 1671 AN: 2102

Alfa AF: 0.797 Hom.: 91438

Bravo AF: 0.834

Asia WGS AF: 0.851 AC: 2959 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.76
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs1555439; hg19: chr20-52809296;