1-46918357-T-C

Variant names:

• chr1-46918357-T-C
• rs4284207

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 0.655 in 151,434 control chromosomes in the GnomAD database, including 34,483 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 0.65 (34483 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99128 AN: 151316 Hom.: 34482 Cov.: 29

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.655 AC: 99139 AN: 151434 Hom.: 34483 Cov.: 29 AF XY: 0.652 AC XY: 48218 AN XY: 73976

African (AFR) AF: 0.414 AC: 17083 AN: 41310

American (AMR) AF: 0.676 AC: 10264 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2670 AN: 3468

East Asian (EAS) AF: 0.518 AC: 2653 AN: 5124

South Asian (SAS) AF: 0.624 AC: 2970 AN: 4760

European-Finnish (FIN) AF: 0.757 AC: 7940 AN: 10490

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.785 AC: 53208 AN: 67790

Other (OTH) AF: 0.691 AC: 1446 AN: 2094

Alfa AF: 0.710 Hom.: 4615

Bravo AF: 0.643

Asia WGS AF: 0.578 AC: 2008 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.31
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs4284207; hg19: chr1-47384029;