rs478801

Positions:

• chr1-110783770-C-T

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 0.848 in 152,224 control chromosomes in the GnomAD database, including 54,856 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 0.85 (54856 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822

ACMG classification

Verdict is Benign. Variant got -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 = 0.969 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: 0.847 AC: 128906 AN: 152106 Hom.: 54795 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.848 AC: 129027 AN: 152224 Hom.: 54856 Cov.: 32 AF XY: 0.851 AC XY: 63318 AN XY: 74430

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.856

Alfa AF: 0.831 Hom.: 6542

Bravo AF: 0.857

Asia WGS AF: 0.940 AC: 3269 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	1.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs478801; hg19: chr1-111326392;