1-55065463-T-C

Variant names:

• chr1-55065463-T-C
• rs597387

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 0.763 in 152,096 control chromosomes in the GnomAD database, including 45,081 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 0.76 (45081 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115996 AN: 151978 Hom.: 45066 Cov.: 31

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.763 AC: 116059 AN: 152096 Hom.: 45081 Cov.: 31 AF XY: 0.769 AC XY: 57162 AN XY: 74348

African (AFR) AF: 0.610 AC: 25275 AN: 41456

American (AMR) AF: 0.857 AC: 13094 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2723 AN: 3472

East Asian (EAS) AF: 0.962 AC: 4968 AN: 5166

South Asian (SAS) AF: 0.868 AC: 4186 AN: 4820

European-Finnish (FIN) AF: 0.826 AC: 8738 AN: 10578

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54384 AN: 68000

Other (OTH) AF: 0.800 AC: 1692 AN: 2116

Alfa AF: 0.773 Hom.: 5441

Bravo AF: 0.759

Asia WGS AF: 0.893 AC: 3105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.37
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs597387; hg19: chr1-55531136; COSMIC: COSV53764075;