chr4-45362897-G-C

Variant names:

• chr4-45362897-G-C
• rs10517133

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 0.107 in 152,182 control chromosomes in the GnomAD database, including 1,093 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 0.11 (1093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.725
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.318 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16264 AN: 152064 Hom.: 1094 Cov.: 32

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.107 AC: 16272 AN: 152182 Hom.: 1093 Cov.: 32 AF XY: 0.110 AC XY: 8168 AN XY: 74380

African (AFR) AF: 0.0863 AC: 3584 AN: 41532

American (AMR) AF: 0.0847 AC: 1294 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3466

East Asian (EAS) AF: 0.331 AC: 1715 AN: 5174

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4818

European-Finnish (FIN) AF: 0.0959 AC: 1016 AN: 10592

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0989 AC: 6726 AN: 68004

Other (OTH) AF: 0.109 AC: 231 AN: 2110

Alfa AF: 0.0959 Hom.: 503

Bravo AF: 0.105

Asia WGS AF: 0.238 AC: 827 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.22
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs10517133; hg19: chr4-45364914;