rs1555439

Positions:

• chr20-54192757-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.795

Alfa AF: 0.791 Hom.: 65448

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555439; hg19: chr20-52809296;