1-55034533-T-C

Position:

• chr1-55034533-T-C

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 0.89 in 152,290 control chromosomes in the GnomAD database, including 60,592 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 0.89 (60592 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135518 AN: 152172 Hom.: 60560 Cov.: 34

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.963

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.890 AC: 135605 AN: 152290 Hom.: 60592 Cov.: 34 AF XY: 0.891 AC XY: 66379 AN XY: 74490

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.964

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.929

Gnomad4 OTH AF: 0.913

Alfa AF: 0.921 Hom.: 87773

Bravo AF: 0.882

Asia WGS AF: 0.939 AC: 3265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2495488; hg19: chr1-55500206;